Wild encounter
Removed this to make more room. It's now in this Pastebin.
Interact
In ORAS you can find (Primal) Groudon (OR) and Kyogre (AS) at level 45 in the Cave of Origin. (Limited)
In ORAS you can find Rayquaza at the top of the Sky Pillar on level 70. (Limited)
In ORAS you can find Latios (OR) and Latias (AS) at Southern Island on level 30. (Limited)
In ORAS you can find Regirock at Desert Ruins on level 40. (Limited)
In ORAS you can find Regice at Island Cave on level 40. (Limited)
In ORAS you can find Registeel at Ancient Tomb on level 40. (Limited)
In ORAS you can find Regigigas at Island Cave on level 50. (Limited)
In ORAS you can find Spiritomb at Sea Mauville on level 50.
In B2/W2 you can find a shiny Haxorus at the Nature Preserve after you have completed the Unova Dex, it is on level 70. (Limited)
In FR/LG, you can find Deoxys Attack (FR) or Deoxys Defense (LG) at Birth Island, it is on level 30. (This requires an event)
In FR/LG, you can find Ho-oh at the top of Navel Rock, it is on level 70. (This requires an event)
In FR/LG, you can find Lugia at the bottom of Navel Rock, it is on level 70. (This requires an event)
In ORAS, you can find one Kecleon in Mossdeep Space Center
In ORAS, you can find one Kecleon in Lavaridge Town
Gift
In ORAS a Team Magma Grunt at the Battle Resort gives you a level 40 Camerupt. (Limited)
In ORAS a Team Aqua Grunt at the Battle Resort gives you a level 40 Sharpedo. (Limited)
In ORAS, Ruby, Sapphire, and Emerald, on Route 101 Professor Birch gives you a level 5 Treecko, Torchic, or Mudkip as your starter Pokemon. (Limited)
In ORAS you can get a level 5 Chicorita, Cyndaquil, or Totodile from Professor Birch on Route 101 after you have entered the Hall of Fame for the first time. (Limited)
In ORAS you can get a level 5 Turtwig, Chimchar, or Piplup from Professor Birch on Route 101 after you have entered the Hall of Fame a second time. (Limited)
In ORAS you can get a level 5 Snivy, Tepig, or Oshawott from Professor Birch on Route 101 after you have completed the Delta Episode. (Limited)
In B2/W2 you get a level 5 Snivy, Tepig, or Oshawott from Bianca in Aspertia City as your Starter Pokemon. (Limited)
In G/S/C, Bill gives you a level 20 Eevee in Goldenrod City. (Limited)
In ORAS Steven (indirectly) gives you a level 1 Beldum in his house in Mossdeep City. (Limited)
In ORAS a scientist at the Weather Institute (Located on Route 119.) gives you a level 30 Castform. (Limited)
In HG/SS Steven Stone gives you a level 5 Treecko, Torchic, or Mudkip in Silph Co. after you have defeated Red. (Limited)
In Platinum, you get level 25 Porygon from a person in Veilstone City.
In HG/SS, you get a Togepi (Egg) in Violet City.
In HG/SS, you can get a level 5 Eevee from Bill in Goldenrod City.
In R/B/Y, a level 15 Lapras is given to you in Silph Co.
In FR/LG, a level 25 Lapras is given to you in Silph Co.
In R/B/Y, you can get a level 30 Hitmonlee or Hitmonchan in Saffron City.
In FR/LG, you can get a level 25 Hitmonlee or Hitmonchan in Saffron City.
In R/B/Y, you can get a level 25 Eevee in Saffron City.
In FR/LG, you can get a level 25 Eevee in Saffron City.
In ORAS, you can get a Togepi (Egg) in Lilycove City.
Portals
(All of the Pokemon in this section are found on level 50.)
In ORAS Ho-Oh (OR) and Lugia (AS) can be found in a portal at Sea Mauville. (Limited)
In ORAS Terrakion can be found at Pathless Plain on Tuesdays and Saturdays. (Limited)
In ORAS Cobalion can be found at Pathless Plain on Sundays, Wednesdays and Fridays. (Limited)
In ORAS Virizion can be found at Pathless Plain on Mondays and Thursdays. (Limited)
In ORAS Cresselia can be found at Crescent Isle. (Limited)
In ORAS Uxie can be found at Nameless Cavern between the times 20:00 and 21:00 or
8:00 PM - 9:00 PM. (Limited)
In ORAS Azelf can be found at Nameless Cavern between the times 21:00 and 03:59 or
9:00 PM - 3:59 AM. (Limited)
In ORAS Mesprit can be found at Nameless Cavern between the times 04:00 and 19:59 or 4:00 PM - 7:59 PM. (Limited)
In ORAS Reshiram (AS) and Zekrom (OR) can be found at Fabled Cave. (Limited)
In ORAS Heatran can be found at Scorched Slab. (Limited)
In ORAS Kyurem can be found at Gnarled Den. (Limited)
In ORAS Raikou can be found at Trackless Forest when it's 00-20 minutes past the hour. (Limited)
In ORAS Entei can be found at Trackless Forest when it's 20-40 minutes past the hour. (Limited)
In ORAS Suicune can be found at Trackless Forest when it's 40-00 minutes past the hour. (Limited)
I don't know where to put
In ORAS you can find Deoxys (Normal Forme) at the Sky Pillar on level 80. (Note that it is not exactly the Sky Pillar on the first encounter, according to Bulbapedia Deoxys is found at the "Edge of space." For re-battles it is found on top of the Sky Pillar.) (Limited)
In Gold, Silver, Crystal, Heartgold, and Soulsilver, you can get Porygon from the Celadon Game Corner.
Trade
In B2/W2, if the player is male, Yancy will trade the player Meowth, Wobbuffet, Ralts, Shieldon, Rhyhorn, West Sea Shellos, Mawile, Spiritomb, Snorlax, Teddiursa, Spinda, and Togepi.
In B2/W2, if the player is female, Curtis will trade the player Mankey, Wobbuffet, Ralts, Cranidos, Rhyhorn, East Sea Shellos, Sableye, Spiritomb, Snorlax, Phanpy, Spinda, and Togepi.
Other Stuff
Mt. Moon's location guide has no information for Gen 1.
Cerulean Cave's location guide has no information for Gen 1.
The Kanto Safari Zone location guide has no information.
Diglett's Cave's location guide has no information for Gen 1.
Rock Tunnel's location guide has no information for Gen 1.
There is no location guide for Kanto's Pokemon Mansion.
Pokemon Tower's location guide has no information for Gen 1.
Kanto's Victory Road's location guide has no information.
Hoenn's Victory Road's location guide has no information for R/S/E.
Seafoam Island's location guide has no information for Gen 1.
Fuchsia City's location guide has no information for Gen 1.
Celadon City's location guide has no information for Gen 1.
Viridian City's location guide has no information for Gen 1.
Bell Tower's location guide has no information for Gen 2.
Sinnoh's Battle Frontier's location guide has no information.
There is no location guide for Hoenn's Battle Frontier.
On Union Cave's page, under "Interact" in both the HG/SS and G/S/C sections, it does not mention that the Lapras can only be encountered on Friday. It also says that the Lapras limited, but a new one appears every Friday. A similar issue is on Valley Windworks' page, but instead of Lapras, the Pokemon that appears every Friday is a Drifloon.
Under "Where to find" on the pages of Omanyte, Aerodactyl, and Kabuto, there is no location listed for R/B/Y. The locations should all be Cinnabar Island.
Under "Where to find" on the pages of Lileep and Anorith, there is no location listed for R/S/E. The locations should all be Rustboro City.
Under "Where to find" on the pages of Omanyte, Aerodactyl, Kabuto, Lileep, Anorith, Cranidos, and Shieldon, there is no location listed for D/P/Pt. The locations should all be Oreburgh City.
Under "Where to find" on the pages of Omanyte, Aerodactyl, Kabuto, Lileep, Anorith, Cranidos, Shieldon, Tirtouga, and Archen, there is no location listed for B2/W2. The locations should all be Nacrene City.
Under "Where to find" on the pages of Omanyte, Aerodactyl, Kabuto, Lileep, Anorith, Cranidos, Shieldon, Tirtouga, Archen, there is no location listed for ORAS. The locations should all be Rustboro City.
Under "Where to find" on the pages of Cranidos, Shieldon, Tirtouga, and Archen, there is no location listed for Sun and Moon. The locations should all be Route 8.
On Cinnabar Island's page, under the "Gift" section for FR/LG, it does not say "Revive [Fossil]" under "Details" for the fossil Pokemon.
On Pewter City's page, under the "Gift" section for HG/SS, it does not say "Revive [Fossil]" under "Details" for the fossil Pokemon.
On Cinnabar Island's page, all of the Gen 1 locations, excluding the trades, are missing.
On Ambrette Town's page, it does not specify what fossil the fossil Pokemon are revived from.
Some Pokemon don't have their Gen 1 locations listed under the "Where to find [Pokemon]" part of their Pokedex page. I've put together this Pastebin of some of the locations that were missed, but it's not complete so I'll add more.
Southern Island's page has no info for ORAS.
Sinjoh Ruins' page doesn't have any info on it at all.
Faraway Island's page has no information for FR/LG on it.
Navel Rock's page has no information for FR/LG on it.
Birth Island's page has no information for FR/LG on it.
On Phione's page, instead of saying "Breed Manaphy or Phione" under the locations section, it just says "Trade/migrate from another game".
On Eterna City's page, it doesn't say that the Togepi that is given to you in Platinum is an egg.
On Route 34's page, it doesn't say that the Pichu, Cleffa, Igglybuff, Tyrogue, Smoochum, Elekid, or Magby that are given to in Crystal you are eggs.
On Violets City's page, it says that Whiscash can be encountered by "Walking in grass or a cave" when a swarm is going on. It actually is encountered on level 10 by fishing with the Old Rod, level 20 when fishing with the Good Rod, and level 40 when fishing with the Super Rod when there is a swarm.
On Violet City's page, it doesn't say that the Togepi given to you in G/S/C is an egg.
There is no info at all on Lavaridge Town's page.
On Fortree City's page, it says that the Plusle you get from trading a Volbeat can only be obtained in Ruby and Sapphire. This is incorrect, as the Plusle can only be obtained in Emerald.
Lilycove City's page has no information for Gen 3.
On the Water Labyrinth's page, it doesn't say that the Togepi given to you is an egg.
Nimbasa City's page has no information at all.
Sprout Tower's location page has no information on it for Crystal, despite Crystal having the same encounters, levels, etc. as Gold and Silver.
The location page for the Whirl Islands have no information on it for Crystal.
National Park's location page has no information on it for Crystal.
Mt. Silver's location page has no information on it for Crystal.
The Ruins of Alph's location page has no information on it for Crystal.
Burned Tower's location page has no information on it for Crystal.
Slowpoke Well's location page has no information on it for Crystal.
Union Cave's location page has no information on it for Crystal.
Ice Path's location page has no information on it for Crystal.
Dark Cave's location page has no information on it for Crystal
Mt. Mortar's location page has no information on it for Crystal.
Mt. Moon's location page has no information on it for Crystal.
Rock Tunnel's location page has no information on it for Crystal.
On the page for Pewter City, it doesn't specify that the Latios/Latias you can find are event exclusive.
Wow, this post is really long.
