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I know there was a question asked just like this for Crystal, but I'd like to know this for all of the Pokémon games.

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If anybody mentions Heracross in DPPt, it's much more complicated than always 1%.
Hey, what about that Heracross in DPPt?
It's one percent on a non-Munchlax tree and 3.5 percent on a Munchlax tree. The location of Munchlax trees is different for each save and determined by the Trainer ID.

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Notes: The listed Pokemon are in alphabetical order for each game. Each Pokemon is followed by the routes/areas where they have a 1% catch rate, and their encounter method. If applicable which game it occurs in and/or the Time of Day will also be listed.
It does not list all the areas where those Pokemon can be encountered, only the locations where their encounter rate is 1%. For example, Raticate does have a 1% encounter rate on Route 11 in Yellow, but it has a 5% catch rate on Route 18, so only Route 11 is mentioned. Only the main series games are included.

Generation I

Since Red/Blue and Yellow have very different catch lists and percentages, I have divided this list between those two games. In this generation, none of the fishing rods have a 1% chance to get anything, so all of the following Pokemon are encountered either in Grass, or by Walking in caves or buildings.

Red/Blue

There were a lot of 1% encounter Pokemon in Red and Blue. Most of these are evolved Pokemon that are very rare in one version, but a lot more common in the other. Doing this did mean that these games had (theoretically) less version exclusives than later entries, but some of the Pokemon that were available were a lot harder to get in one version than the other. The main exceptions to this is, of course, the nightmarish task of catching certain Safari Zone encounters (especially Chansey!).

  • Caterpie: Route 25, Grass, Red Only
  • Chansey: Safari Zone (Central Area), Walking
  • Clefairy: Mountain Moon (1F), Walking
  • Dewgong: Seafoam Islands (B3F), Walking
  • Ditto: Cerulean Cave, Walking
  • Golbat: Seafoam Islands (B4F), Walking
  • Golduck: Seafoam Islands (1F and B2F), Walking, Red Only
  • Graveler: Victory Road (2F), Walking
  • Haunter: Pokemon Tower (3F only), Walking
  • Kangaskhan: Safari Zone (Western Area), Walking
  • Kingler: Seafoam Islands (B1F), Walking, Blue Only
  • Marowak: Victory Road (1F), Walking
  • Muk: Pokemon Mansion (all floors), Walking, Red Only
  • Pinsir: Safari Zone (Eastern Area), Walking, Blue Only
  • Scyther: Safari Zone (Eastern Area), Walking, Red Only
  • Seadra: Seafoam Islands (B1F), Walking, Red Only
  • Slowbro: Seafoam Islands (1F and B2F), Walking, Blue Only
  • Tauros: Safari Zone (Northern Area), Walking
  • Weedle: Route 25, Grass, Blue Only
  • Weezing: Pokemon Mansion (all floors), Walking, Blue Only

Yellow

Yellow had less 1% encounters than Red and Blue, but this is largely because it is only a single game, and so avoided the "version exclusive" encounters of the other Generation I games.

  • Chansey: Safari Zone (Central Area), Walking
  • Clefairy: Mountain Moon (1F), Walking
  • Dodrio: Route 17, Grass
  • Fearow: Route 9, Grass
  • Pidgeotto: Routes 24 and 25, and Viridian Forest, Grass
  • Pinsir: Safari Zone (Northern Area), Walking
  • Raticate: Route 11, Grass
  • Scyther: Safari Zone (Eastern Area), Walking
  • Slowbro: Seafoam Islands (B2F), Walking
  • Tangela: Safari Zone (Western Area), Walking
  • Venomoth: Routes 14 and 15, Grass

Generation II

Generation II did add several new methods to encounter Pokemon (Rock Smashing rocks and Headbutting trees), but none of these gave encounter rates of 1%. Several new mechanics that altered encounter rates were introduced, however - Time of Day and Swarms - and these did affect Pokemon with a 1% encounter rates. For Time of Day, the Pokemon in question were generally a lot common at another time of day (e.g. Quagsire and Zubat are both more common at Night). Swarms are more interesting, as that meant that at certain times Pokemon with very low encounter rates were a lot more common for a short period of time. Of the 1% Pokemon, this could affect Yanma, Dunsparce, Marill, and Snubbull, so those Pokemon's encounter rates assume that there is no swarm of them at the time.

Gold and Silver

  • Aerodactyl: Route 14, Trade
    Technically, I am cheating by including Aerodactyl on this list, since it is a trade, and so a definite encounter. However, you need to trade a Chansey for it, and since Chansey is so rare, it may as well be a 1% encounter!
  • Chansey: Routes 13, 14, 15, Grass
  • Dunsparce: Dark Cave (Violet City side), Walking
  • Marill: Mt. Mortar (Entrance), Walking
  • Quagsire: Route 26, Grass, Morning Only
  • Snubbull: Route 38, Grass
  • Yanma: Route 35, Grass
  • Zubat: Route 32, Grass, Morning Only

Crystal

  • Aerodactyl: Route 14, Trade
    Technically, I am cheating by including Aerodactyl on this list, since it is a trade, and so a definite encounter. However, you need to trade a Chansey for it, and since Chansey is so rare, it may as well be a 1% encounter!
  • Chansey: Routes 13, 14, 15, Grass
  • Dunsparce: Dark Cave (Violet City side), Walking
  • Jynx: Ice Path (1F and B1F), Walking, Morning and Day Only
  • Pupitar: Mt. Silver (Summit), Walking, Day Only
  • Sneasel: Ice Path (B1F), Walking, Night Only
  • Weezing: Burned Tower (B1F), Walking
  • Yanma: Route 35, Grass

Generation III

Ruby and Sapphire

  • Electrode: New Mauville (Basement), Walking
  • Illumise: Route 117, Grass, Sapphire Only
  • Kecleon: Routes 118, 119, 120, 121, 123, Grass
  • Magneton: New Mauville (Basement), Walking
  • Surskit: Routes 102, 111, 114, 117, 120, Grass/Surfing
  • Tentacruel: Abandoned Ship, Surfing
  • Volbeat: Route 117, Grass, Ruby Only
  • Wailord: Route 129, Surfing

Emerald

Note that Area 5 of the Safari Zone is the area to the far southeast, and is only accessible after entering the Hall of Fame.

  • Electrode: New Mauville (Basement), Walking
  • Goldeen: Routes 102, 111, 114, 117, 120, Surfing
  • Kecleon: Routes 118, 119, 120, 121, 123, Grass
  • Magneton: New Mauville (Basement), Walking
  • Nuzleaf: Route 114, Grass
  • Octillery: Safari Zone (Area 5), Super Rod
  • Quagsire: Safari Zone (Area 5), Surfing
  • Seedot: Routes 102, 117, 120, Grass
  • Tentacruel: Abandoned Ship, Surfing
  • Volbeat: Route 117, Grass
  • Wailord: Route 129, Surfing

FireRed and LeafGreen

Note that for Unown certain letters only have a 1% chance of spawning. Specifically, these are the '?' '!' and 'O' Unown symbols.

  • Chansey: Safari Zone (Entrance Area), Grass
  • Clefairy: Mt. Moon (1F), Walking
  • Dragonair: Safari Zone (All Areas), Super Rod
  • Kakuna: Routes 24 and 25, Grass, LG Only
  • Koffing: Celadon City, Surfing
  • Golduck: Seafoam Islands (B3F and B4F), Surfing, FR Only
  • Grimer: Celadon City, Super Rod
  • Haunter: Pokemon Tower (3F), Walking
  • Kangaskhan: Safari Zone (Area 3), Grass
  • Lapras: Icefall Cave (Back Cave), Surfing
  • Metapod: Routes 24 and 25, Grass, FR Only
  • Nidoran-female: Route 3, Grass, FR Only
  • Nidoran-male: Route 3, Grass, LG Only
  • Pinsir: Safari Zone (Area 1), Grass, LG Only
  • Psyduck: Routes 4, 10, 11, 12, 13, 19, 20, 21, 24, Pallet Town, Cerulean City, Vermilion City, Vermilion Harbor, Cinnabar Island, One Island, Treasure Beach, Kindle Road, Bond Bridge, Icefall Cave (Back Cave), Five Isle Meadow, Memorial Pillar, Resort Gorgeous, Five Island, Water Labyrinth, Water Path, Green Path, Outcast Island, and Tenoby Ruins, Super Rod, FR Only
  • Scyther: Safari Zone (Area 1), Grass, FR Only
  • Slowbro: Seafoam Islands (B3F and B4F), Surfing, LG Only
  • Slowpoke: Routes 4, 10, 11, 12, 13, 19, 20, 21, 24, Pallet Town, Cerulean City, Vermilion City, Vermilion Harbor, Cinnabar Island, One Island, Treasure Beach, Kindle Road, Bond Bridge, Icefall Cave (Back Cave), Five Isle Meadow, Memorial Pillar, Resort Gorgeous, Five Island, Water Labyrinth, Water Path, Green Path, Outcast Island, and Tenoby Ruins, Super Rod, LG Only
  • Tauros: Safari Zone (Area 2), Grass
  • Unown: Tanoby Chambers, Walking
  • Wobbuffet: Cerulean Cave (B1F), Walking

Generation IV

Several new methods of catching Pokemon were added in this generation, as well as the return of the previous capture methods. The ones that have 1% chance to encounter a Pokemon are Honey Trees and the Poke Radar. The Poke Radar is only given after getting the National Dex. Honey is a very annoying method. There are 21 Honey Trees in the game, but 4 will have a different encounter list than the other 17. To differentiate between these (when required) the 4 different Honey Trees will be called "Honey Tree (Special)". Which Honey Trees are special will be randomly chosen for every new game, however. The Honey Tree Pokemon with a 1% chance will have no locations given, since they can be encounter in any Honey Tree or Special Honey Tree.
Swarms again return, as well, which still increases the chance of encountering some of the listed Pokemon for a short period of time.

Diamond and Pearl

  • Azurill: Great Marsh (Areas 1, 2, 3, 4, and 6), Grass
  • Bidoof: Great Marsh (Areas 1, 2, 3, 4, and 6), Grass
  • Heracross: Honey Trees (Normal)
  • Kirlia: Routes 203 and 204, Poke Radar
  • Munchlax: Honey Trees (Special)
  • Shellos: Route 224, Grass

Platinum

  • Beautifly: Route 205 and Eterna Forest, Grass
  • Chimecho: Mt. Coronet (5F), Walking
  • Dustox: Route 205 and Eterna Forest, Grass
  • Gastrodon: Route 213, Pastoria City, and Canalave City, Surfing
  • Golbat: Oreburgh Gate (B1F), Walking
  • Heracross: Honey Trees (Normal)
  • Munchlax: Honey Trees (Special)
  • Pelipper: Routes 219, 220, 221, 222, and Sunnyshore City, Surfing
  • Tentacruel: Routes 205 and 212 (South), Surfing

HeartGold and SoulSilver

  • Chansey: Routes 13, 14, and 15, Grass
  • Dunsparce: Dark Cave (Violet City Entrance), Walking
  • Marill: Mt. Mortar (Entrance), Walking
  • Snubbull: Route 38, Grass
  • Yanma: Route 35, Grass

Generation V

There are very few 1% encounter Pokemon in either of the Unova games. Aside from those mentioned below, most encounters have a minimum of 5% chance to encounter (or 2.5% chance if you want to take into account the gender differences of Pokemon like Jellicent or Unfezant). In addition to the 1% encounters below, Tynamo is the only other one with a lower encounter chance (2% on several of the floors of Chargestone Cave).

I think the lack of rare encounters is due to the introduction of the "special" encounter methods. Whenever you are are near grass or water, or in a cave, there is a small chance of rustling grass, rippling water, or dust clouds, respectively, appearing. These "special" encounters contain different Pokemon than are normally found on the route. If a Pokemon in a "special" encounter has a 5 or 10% chance to appear, then you could still be searching for it for a very long time, so it really may as well be a 1% chance.

Seasons may also change the encounter rate for some Pokemon (usually just between Winter and the rest of the seasons). Every month is a new season (so the cycle doesn't match the actual seasons in the real world).

Black and White

  • Chinchou: Route 18, Fishing
  • Cryogonal: Twist Mountain, Walking, Spring, Summer, and Autumn Only
  • Dragonite: Dragonspiral Tower (Outside), Fishing in Rippling Water

Black 2 and White 2

  • Dragonite: Dragonspiral Tower (Outside), Fishing in Rippling Water
  • Mienfoo: Dragonspiral Tower (Entrance), Dark Grass, Winter Only

This answer is continued in a separate post below.

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edited by
Since you gave me the BA I will continue building on this answer when I have time until it is actually complete. It may take a few days, though.
This is quite a task lol.
6 votes

1st Generation
Red and Blue

Yellow

2nd Generation
Gold, Silver and Crystal
Snubbull, Route 38
Quagsire, Route 26
Chansey, Routes 13, 14 and 15
Marill, Mt. Mortor 1F
Dunsparce, Dark Cave (near Violet city)

3rd Generation
Ruby, Sapphire, and Emerald
Surskit, Routes 102, 117, 114, 120
Volbeat, Route 117
Illumise, Route 117
Kecleon, Routes 118, 119, 120, 121, 123
Wailord, Route 129
Electrode, New Mauville Basement
Magneton, New Mauville Basement
FireRed and LeafGreen
Nidoran F, Route 3
Nidoran M, Route 3
Clefairy, Mt Moon 1F
Psyduck, Routes 4, 24, 11, 10, 12, 13, 21, 19, 20, Cinnabar Island, One Island, Treasure Beach, Kindle Road, Icefall Cave Inner Section, Icefall Cave Rear, Resort Gorgeous, Water Labryinth, Five Isle Meadow, Memorial Pillar, Outcast Island, Green Path, Water Path, Trainer Tower, Tanoby Ruins (FireRed, Super Rod)
Slowpoke, Routes 4, 24, 11, 10, 12, 13, 21, 19, 20, Cinnabar Island, One Island, Treasure Beach, Kindle Road, Icefall Cave Inner Section, IcefallCave Rear, Resort Gorgeous, Water Labryinth, Five Isle Meadow, Memorial Pillar, Green Path, Outcast Island, Water Path, Trainer Tower, Tanoby Ruins (LeafGreen, Super Rod)
Metapod, Routes 24, 25 (FireRed)
Kakuna, Routes 24, 25 (LeafGreen)
Grimer, Celdadon City (Super Rod)
Koffing, Celadon City (Surf)
Haunter, Pokemon Tower 3F, 4F, and 5F
Dragonair, Safari Zone Entrance, Safari Zone Area 1, 2, 3 (Super Rod)
Chansey, Safari Zone Entrance
Scyther, Safari Zone Area 1 (FireRed)
Pinsir, Safari Zone Area 1 (LeafGreen)
Tauros, Safari Area Zone 2
Kangaskhan, Safari Zone 3
Golduck, Seafoam Islands B3, B4 (Surf, FireRed)
Slowbro, Seafoam Islands B3, B4 (Surf, LeafGreen)
Lapras, Icefall Cave Rear (Surf)

4th Generation
Diamond and Pearl
None
Platinum
Dustox, Eterna Forest, Route 205 North
Beautifly, Eterna Forest, Route 205 North
Golbat, Lost Tower 3F
Gastrodon, Route 218 (Surf)
Chimeco, Mt Coronet 5F, Turnback Cave 3
Dusclops, Turnback Cave 3
HeartGold and SoulSilver
Dunsparce, Dark Cave (Violet Entrance)
Yanma, Route 35
Snubbull, Route 38
Remoraid, Route 44 (Good Rod)
Chansey, Route 15, 14, 13
Marill, Mt Mortar 1F

5th Generation
Black and White
Cryogonal, Twist Mountain 1F
Dragonite, Dragonspiral Tower Moat (Fish, Special)


Work in progress.

by
In Emerald, Seedot has a 1% encounter rate in routes 102, 117, and 120. In DP, Shellos has a 1% encounter rate in route 224. In Platinum, there's a Pokemon with a 1% encounter rate in just about everywhere accessible before the national Pokedex and is connected to the ocean (Tentacruel on route 205 and route 212, Gastrodon on route 213, etc.). You definitely missed some more.
Trust me, I know I missed some. As I said, work in progress.
Allow me to rant about the 1% encounter rate of Chimecho in Emerald's Mt. Pyre. 9-year-old me tried so hard to complete her Pokedex and I spent ages trying to get it! Then I found it and caught it and cried.
Wait Dunsparce is 1% encounter rate? I saw two of those back-to-back. If i had known they were rare I would have caught them then ;~;
According to Bulbapedia, Chimecho have a 2% encounter rate on Mt. Pyre in Generation 3. Dunsparce have an 80% encounter rate when smashing rocks.
Thanks for the up votes, even though this is severely incomplete lol.
5 votes

This is a continuation of my answer above. I hit the maximum word limit, so it wouldn't let me post everything as one answer.

Generation VI

X and Y

Most of these Pokemon have forms that only have a 1% chance of appearing, but they have other forms that appear more commonly. This means that Pokemon like Flabebe, Pumpkaboo, and Rotom may not truly have a 1% chance of appearing, but certain forms of those Pokemon do.

  • Abomasnow: Route 17, Snow
  • Flabebe (white flower): Routes 4 and 7, Grass
  • Lapras: Route 12 and Azure Bay, Surfing
  • Pumpkaboo (Super Size): Route 16, Tall Grass
  • Rotom (Fan, Frost, Heat, Mow, and Wash forms): Lost Hotel, Shaking Trash Cans, Tuesday Only
    Note: the Rotom forms, according to Bulbapedia, have a "very rare" chance of appearing, with the normal Rotom form being common. However, these forms are easily obtained by catching the normal Rotom and changing its form manually. Since Bulbapedia doesn't list an exact percentage, this is just a guess, but I imagine the chance is around 1%.

OmegaRuby and AlphaSapphire

There are very few 1% chance Pokemon in ORAS, and a lot less than the original Ruby and Sapphire. I have no included any of the special encounters you can get through the Dex Nav after beating the Elite 4, simply because their percentages have not been confirmed (at least not on Bulbapedia).

  • Mantine: Battle Resort, Surfing
  • Pelipper: Sea Mauvile (Outside), Surfing
  • Surskit: Routes 102, 114, and 117, Grass

And with that this list is finally finished!

Sources: Searching through the individual route and location pages on Bulbapedia.

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*tumultuous applause*
Great job finishing this :)
Do Sun/Moon next!