1) Slaking: I'm just going to get this out of the way, I HATE MONKEYS. They're ugly and gross and smelly and they throw their own shit everywhere. But at the same time, I kept on having trouble with stallers. As in, every damn opponent I fought was determined to drag out the match and get me to ragequit. So, I forced myself to raise one because I knew a Choice Band Giga Impact set would OHKO most tanks even in OU. As it turns out... I was right. Now he's a mainstay on my team and I've even grown to like that goofy-looking old man a bit.
2) Blaziken: When I first saw it, I wondered what the heck was going on with the design. I had a fluffy chicken and then it turned into this thing. Theeeen... well, I discovered the internet. *blush* I fell in love with the design in more than one way.
3) Mewtwo: When I was a kid, I had these huge Mew vs. Mewtwo "debates". I liked Mew better because it was cuter. (Yeah, I was and still am a very girly boy.) Then came Super Smash Bros. Melee - as awful as his metagame turned out to be, he fit my playstyle pretty well, and I enjoyed playing as him a lot. And after that came Mega Y and Pokémon-Amie, and... well, I never thought I'd actually be calling Mewtwo "cute".
4) Medicham: I didn't like his design. I thought it looked goofy and sort of racist. But in Pearl, he worked damn well with Recover and Hi Jump Kick, and he soon became my first-ever Level 100.
5) Ponyta/Rapidash: I didn't hate them as much as think they were just forgettable. But then I was part of a crossover-supporting MLP:FiM roleplay board, and I made a Ponyta character for the heck of it, one that was adorably affectionate and hilariously innocent and naiive. Me and everyone else there grew pretty attached to her, so, even though I don't use them competitively, they've become very high up on my list of favorites.