Hitmonchan... I have told the story on how he became my favorite many times. But it was just this odd attraction I felt to him. Not like romance attraction, like finding somebody's hidden appeal. Have you ever looked at a Pokemon who doesn't seem all that amazing and feel a sort of fondness to it?
Closely following Hitmonchan, I adore Electabuzz and Machoke. I think I may like Machoke more because it tends to get bashed and abused in the anime and most people dislike it, so I feel I need to protect Machoke. I wish Machoke didn't evolve and have evolved stats so I could use one on a team. A FEMALE one!
Ones I also like to a lesser extent: Exeggutor, Bulbasaur, Ponyta, Flygon, Blaziken (not because he's cool or whatever, he's just a neat looking anthro), Breloom, Nidoking, Houndoom, Granbull, Meowth, Diglett, Ledian, Heracross, Tyranitar, Steelix, Lapras, Golduck, Exploud... probably more.