Sooo many choices! Guess I'll choose four.
I'll start with the obvious: Buizel/Floatzel, of course. ^-^ I've always liked buizel since it was first revealed (I think for the ninth movie). I find them adorable, and being a "comic artist," I absolutely love that they can easily show a wide range of emotions. Floatzel also got the honor of being the first pokémon I've EV-trained and bred with nature and IVs in mind. (Oh, if only my old Bui/Floatz fan club members were still around! )
I also have to choose Mudkip/Marshtomp/Swampert. Not for the meme. I actually find them cute in a way, I guess endearing. Yes, even the awkward marshtomp and monster-ish swampert. I grew especially fond of marshtomp for some reason. Maybe it was the scene in PokéSpe where Zuzu was wearing the sweater?
There's also Wooper/Quagsire. Those perpetual smiles of derpiness! :D That's all I have to say.
And finally, Oshawott/Dewott/Samurott. I believe it was dewott that really got me on this ship. When it was revealed, it actually swayed my choice of starter in fifth gen (I always choose based on the unevolved stage). But my brother already took oshy, so I didn't change. It has that fierce expression and cool form, yet appeals to my kind of cute. I quickly grew to love oshawott, and samurott was an interesting final form (with hidden seamitars!), so yeah. Gotta vote for them too.
Honorable mention to squirtle, my favorite Gen I pokémon. Wartortle's alright, but I'm not really too fond of blastoise, so no vote there. D: