Ninetales: Especially the shiny version, Ninetales is easily my favorite Pokemon of all time. It's based on one of my two favorite animals, it's extremely beautiful and elegant, it performs uniquely for a Fire-type, it's got excellent mastery of simplicity in its design, and it's got nostalgia going in its favor as well.
Xerneas: The only Pokemon to ever really, really give Ninetales a run for its money as my favorite. It still falls as number two, but only barely. I elaborate more on why I love Xerneas so much in the Favorite 3 Legendaries thread.
Dewott: I love him so much and I don't completely know why. He's my favorite type, he's a badass little "I'm tough, fear me!" kind of guy, but that also makes him precious because he really isn't that tough. Everything about its design just works for me.
Nidoking: I've always adored Nidoking, since the very beginning. There's just something so amazingly perfect about its design. It's a giant poisonous dino-bunny with one of the most impressive and fun movesets of any Pokemon in the entire series. It's absolutely vicious looking, but can be very gentle and friendly looking as well... and the shiny is perfection. @_@
Dragonair: Elegance in its purest form, Dragonair is just amazing. A master of simplistic design, iconic in the ideal of the dragon typing, and reasonable diverse in its usefulness. Sadly I don't care for Dragonite much, so evolving it is usually kind of an ordeal. Either I permanently change one of my favorite Pokemon so it can be usable, or I leave it fairly weak. Still yet to raise a Dragonite as a result.
Glaceon: My favorite Eeveelution, formerly Vaporeon, Glaceon is an ice fox... that's really all I need to say about it. I love foxes and I adore ice. It's adorable, it's elegant, and it's simple. Sadly... it's pretty mediocre competitively, but usefulness is never why I favor things.
Clawitzer: I love crustaceans, they're my favorite kind of aquatic creature, and I feel a connection to them as a species. Clawitzer is my favorite of the crustacean Pokemon... and considering I ADORE all of them, that says something. My favoritism likely comes from my having used it extensively in X. It's the first Pokemon in that game I set out to specially train, and I even raised a second one after breeding it to perfection because I loved it that much.
Fletchinder: Normally something I'd have overlooked, and I did for awhile, but... then Amie took my attention. Fletchinder isn't something I ever expected to like because it's not as 'cool' or powerful as Talonflame, but it's not as cute as Fletchling... or is it? Fletchinder has Flame Body, so I spent a lot of time with it while breeding, and in that time I eventually got bored and decided to play with it in Amie... OH... MY... GOD... It was so adorable I almost teared up. The little head bobbing dance it does, the cute way it 'smiles', the way it peaks around the corner at you sometimes (I'm pretty sure all Pokemon do these things but it was just precious with Fletchinder.) I think what took me by the most surprise was how unexpected it was. I really didn't expect to pay ANY considerable attention to it, but I am so glad I did. I love my Lv.100 Fletchinder so much. @_@
There are so many more I could name, but I'd be at it forever. There's at least thirty Pokemon that I love so much I always feel bad for not mentioning them.