This thread has been an interesting read!
I have a couple...
Meganium -- I was so proud in grade school that I had a level 92 one, it was the highest level out of all of my friends' Pokemon. I don't use one anymore but it's my favorite grass type.
Vaporeon -- the first Pokemon I got to level 100. I have a thing for water types (who would've guessed) and a generic soft spot for eeveelutions so this one's a shoe-in for my favorite.
Mawile -- I have no idea why I like this little guy so much. His stats suck and he's just all-around pretty useless... but I really like his design and I think he's cute. I dunno, haha.