I have lots of favorites, and here's explanations for some of them...
Ninetales: That's where I got my username here at Pokecommunity! I like Ninetales because of its powerful flame and mysteriousness. I was drawn towards it by the Pokemon episode where Ash and friends visited a fake mansion created by Ninetales's illusions (forgot episode name). And it's a Fire-type, my third favorite type.
Gardevoir: I fell in love with Gardevoir ever since I got it in Sapphire. I love the way it looks, and it's a good Pokemon to have in the game (after you painfully evolve it from a Ralts and a Kirlia...). Sort of like Alakazam, with higher Special Defense! And Gardevoir wouldn't be a bad Pokemon to have around--especially if it would risk its life to protect its trainer...
Banette: It was my sadistic nature that drew me towards this Pokemon. I fell in love with it ever since I used it in a fanfic, where this old woman named Celia used it to constantly curse her great-granddaughter Kelsey. But other than that, I don't know why I like Banette so much...
Alakazam: I totally agree with Linksocc. Alakazam is a cool Pokemon, but I like it for more than its special attack. Alakazam would be useful for getting to places quickly because it can teleport. It's also the smartest Pokemon there is--another reason why I like it... (5000's pretty darn high for an IQ!) And it's the best Pokemon of Sabrina, my favorite trainer! And it's a Psychic-type, my favorite type! Hmmm...
Bellossom: Bellossom is so cute! And it's a good dancer too! That's why I like Bellossom, even though I don't think it's a really good Pokemon in the game because of its lousy speed and not much else...
Xatu: I like Xatu because it can predict the future, but also because of its daily routines. Wake up, stare at the sun, meditate, peek into the past and future... all day long... Huh, wish I could do that... Meditite would have also been my favorite Pokemon, but there's something about Xatu I like better. It has a better appearance, better attacks, and it's a bird and I like birds...
Hypno: I fell in love with Hypno when I got it as my best Pokemon in Yellow. Without it, I couldn't have beaten the Elite 4! I also like Hypno for its hypnotic abilities, far superior to that of any other Pokemon I know of... I kind of got mad when I heard that Hypno is not a good Pokemon in the game because of its lousy speed, but who cares? And it doesn't appear in Ruby/Sapphire... Darn! Oh well, I always liked Hypno anyways!
Misdreavus: I like Misdreavus because of its mischievous personality and its cute and mysterious appearance. I sort of wish Misdreavus would have better attacks in the game, but... I immediately fell in love with it when I saw it in Pokemon Stadium 2. And it's a Ghost-type, my second favorite type!
Dragonair: This is my only favorite Pokemon that isn't fully evolved. That's because I like Dragonair's appearance more than Dragonite's... Dragonair looks more mysterious, and I like mysterious Pokemon. It's a Dragon-type, my fourth favorite type! I also like the way it moves when it flies--it just floats in the air. The spheres on its neck and tail must be awfully pretty too... Dragonite seems too much of a "musclehead" to me anyways, and well, too stereotypical... Sorry if I offended you Dragonite lovers... :disappoin
I like those Pokemon so much that I put them all in my new Pokedex (except for Banette), and I even created evolved forms for some of them!