Ok so I've kind of been waiting for this question because I love this topic. I'm not going to count spin off games.
We should start off by saying that the chance of a Pokemon being shiny is never below 1/8192, at least in the main series games. There are glitches in GSC that can cause shinies of specific Pokemon to become much much much much rarer, but I won't be talking about that either. I also will be completely disregarding Masuda Method as a viable option to get shinies.
This means we will be talking about the chance of finding the Pokemon in the wild and multiplying it by the shiny chance to find our odds of finding this Pokemon. I will also be taking time into account, especially for number 2.
1 is obvious, and if you want me to get rid of this I will, and I'll add a new #10. The chance of getting a specific shiny Spinda variation in HGSS via Hoenn Sound is a 0.000000000000058128720% chance. That's 1/4,200,000,000 x 1/8192 x 1/5. I'd like to see you go for this one ty.
2 is Pokemon Ranger Manaphy. Even though it is a guaranteed encounter, it takes an average of 11 hours to have one single encounter, not even counting how long it takes to trade and hatch the egg, (which takes an extremely long time.) This means it takes approximately 90,000 hours of gameplay to reach shiny odds for this hunt. So even though it has base odds for a guaranteed encounter, I think most people would agree that this is the hardest shiny hunt besides Mr. spinda.
3 is a DPPt Shiny Munchlax. This is pretty self explanatory. 4/21 trees have a Munchlax in them, and you can figure out two of them without cheating, but still, it's a 1% chance every six hours. A 1/819,200 chance of finding a shiny, when you get 8 encounters, (two known trees) at maximum per day is ridiculous. This means it takes approximately 281 YEARS if you’re just using one DS.
4 is a Star Shiny Authentic Sinistea.
Authentic Sinistea has a 1% encounter rate in two different locations, (Glimwood Tangle and Old Cemetery,) however it can be found as a visible encounter in the Old Cemetery. This means this hunt is only this rare for people without the expansion pass, as the Old Cemetery is in CT. And a wild encounter has 1/16 chance of being a Star Shiny and a 15/16 chance of being Square Shiny. 1/4096 x 1/100 x 1/16 = 0.00000152587% chance of encountering. That would take 54,613 hours to reach odds. And I know I am not considering breeding as a possible aspect, but it should be noted that it is impossible to hatch an Authentic Sinistea from an egg
5 is Honey Tree Female Combee/Vespiquen in DPPt. Again, Combee has a standard 1/8192 odds of being found, but it takes 6 hours to get a single encounter, and at best you have a 40% chance of finding a Combee at a tree, and a 10% chance for nothing at all to appear. And then you have to find a female which is a 12.5% chance. Combining all these odds (1/8192 x 2/5 x 1/8) gives a 0.000610351% chance. Or you could go with a 20% chance for a Combee in a honey tree and get a 0.000305175% chance. Not to mention the 49,000 hours it takes to reach shiny odds just for every Pokemon encounter you have, whether it's Combee or not. I'm going to go with the 40% odds, because I'm looking for the worst odds for the best encounter chance for a Pokemon in a respective game. Honey trees are the only way to find Combee in DPPt besides breeding, plus the fact it takes 6 hours to get another.
6 is Bonus Disk Jirachi from Colosseum. This hunt is nearly identical to Manaphy, except it takes about 20 minutes instead of 11 hours. So it takes about 2730 hours to get this one. This is only behind Combee because Combee takes a lot more time.
7 is a Void Glitch Arceus. I'll let 16ferraran from Reddit explain it for me.
In DP, there exists a glitch involving the tiles. A specific combo of movements will cause nearby tiles to load incorrectly and there will just be a void of blackness. By walking thousands of steps in the void, the player will be able to encounter Arceus. (If you have questions, please search on YouTube) But then you ask, why can't you use the glitch to get to the Hall of Origin and unlock the event?? Well, once you arrive there, you'll get stuck on the edge and you won't be able to get to where you need to go without using the walk through walls cheat, which then ends the legitimacy aspect of the hunt. The only way to encounter a legit Shiny Arceus nowadays is to save the game during of the steps in the void (Please research on your own as this is very difficult to explain). Saving in any other area of the void will have unpredictable effects, and could erase your save file. After saving, another movement combo involving a few thousand more steps will need to be performed before you can actually encounter your legit Arceus. The soft reset takes about 5:30.
So imagine doing about the second half of the void glitch 8192 times before reaching odds for this Pokemon. That's about 751 hours to reach odds. Not to mention the fact that messing up the Void Glitch just one out of your thousands of encounters could ruin your save file permanently.
8 is Legendary Event Zoroark in Black and White. Now, I know that this encounter is standard 1/8192, but, your asking for the rarest shinies. The only way to get Zoroark in BW is via Pokemon from events in Gen IV, which you would then have to transfer to BW. These events include Shiny Entei, Raikou, and Suicune, who were distributed for a week each 10 years ago. These events obviously don't exist anymore, and the DNS server exploit for Gen IV is known to be very unreliable. So unless you still have one of these event Pokemon from 2010-11, the chances of you being able to go for this hunt is 0. It also should be noted that the illusion of the Legendary Beast that Zoroark transforms into can be shiny, but when Zoroark reverts to his normal form, the shininess can go away. But that doesn't affect odds.
9 is a 2001 Shiny Celebi. First off, you could only do this in Japan. Then you had to buy a limited edition GB cable that connected to a Japanese exclusive Pokemon mobile phone thing. Then you have to acquire all 16 badges, complete a mini game and a quiz, and only then will the attendant at the Pokemon Center give you a GS Ball. Then you have to take it to Kurt, wait a day, and finally, go to the Ilex Forest Shrine. From there you soft reset. This is ridiculously difficult because this entire process had to be done in Japan in 2001.
And finally number ten is a Gen 1 shiny. I put this one at the bottom of this list, because there are plenty of ways to manipulate this, but without outside knowledge/manipulation, it is incredibly difficult. This is a Gen 1 shiny. You know how these work. But this is the kicker. The ratio of shiny to non-shiny IV spreads in Gen I is 1/8192 (it's technically incorrect to say this is the "chance" of finding a shiny due to how the RNG works, but it's close enough). However, due to a quirk in the Gen I RNG, normal wild encounters in grass, caves, or water will never have an IV spread that results in shininess, and so only static and fishing encounters, in-game trades, and gift Pokémon can have shiny IVs in Gen I. On top of the fact that you can't tell if it's even shiny unless you transfer it to Gen 2.
Sheeeeesh that took some work.
Source
