Wow, I missed quite a few of these. >_< So let's vote for seven of them!
Murkrow/Honchkrow - I really like their designs and the ideas behind them. Witchy murkrow make up the members of honchkrow's mafia and all that.
Gligar/Gliscor - They're cute. Even gliscor, though that took me a bit to get used to. Doesn't hurt that I like using them in battle too.
Taillow/Swellow - More swellow, though I like them both. Swellow's cool, with that suave hair thing going on and its speed.
Swablu/Altaria - Cute and gentle, opposite from the usual connotation of altaria's dragon-typing. I'm not a fan of dragon-types for their straightforward brute strength, so altaria's a breath of fresh air. >_<
Emolga - It's really my brother that got me to really notice how adorable it is. Also, I really love the one in PMD: Gates to Infinity.
Chatot - Very unique bird, what with Chatter and all. I like its bright colors and the musical design. And I think I'm one of the few people that like Chatot in PMD: Explorers. His sacrifice in Brine Cave always makes me tear up, haha.
Other: Natu/Xatu - Their totem pole/native-ish design is really neat! I remember doodling xatu a lot in sixth grade, before Gold and Silver were released outside of Japan.