What are some of your favorite alternate universe versions of the Mane Six, the villains, or any other characters?

For example, do you prefer Celestia becoming the evil Daybreaker and an uncorrupted Luna banishing her to the Sun? Or perhaps a Twilight who focused on science instead of magic?

6186096
Wow, what a huge question.
To think of my favorite versions, I'd have to go through my favorite stories, because if I'm going to like an alternate version of a character, I'd probably end up liking the story too.

There are a lot to choose from, personal highlights include that one fic where Fluttershy is a dragon princess, Rarity is pirate, and those are the least weird things in the story (dead fic), the one where Fluttershy is a samurai (also dead), any fic where X is a Time Lord, this fic with Apple Bloom as a changeling (dead), the version of Scootaloo that dies a bunch (is aptly dead), the one where Pinkie is Sherlock Holmes (dead), the one where everyone is a British stereotype (dead), the versions of Twilight and Sunset that live in a hard sci-fi universe, the Chrysalis that works at Quills and Sofas, the one where baby Rainbow is adopted by Iron Man, the one where Celestia is Windigo, Princess/Queen Rarity and Bodyguard Twilight ship AU, the one where Rainbow becomes Superman, yeah this one, this one too, the one where Diamond Tiara adopts Scootaloo as a daughter, this one with spies, and one of the "Fluttershy is a vampire" fics.

Oh, and every other "X is a changeling" fic. As you can see, there are a lot of weird AU versions of characters that I like.

6186096 Well I am a big fan of Pinkie Pie in the fic Seeing the Pattern. In this fanfic Pinkie Pie and Pinkamena are two different personalities, with Pinkie Pie being the happy party planner by day and Pinkamena being the grumpy mare who has the ability to see the grim reaper by night. Throughout the flic Pinkamena is trying to thwart death and keep Ponyville safe.

The fact that Pinkie Pie likes sweets and Pinkamena likes salty/bitter foods is also really interesting.