I'm gonna be very predictable, but the cutest pokemon for me is definitely Poochyena:
..for obvious reasons! :3
Namely that it looks like a fluffy puppy ! And even its voice acting in the anime is adorable! It doesn't even say syllables most of the time and just makes high pitched noises ! Watch "A Bite to Remember" to see what I mean ! :D
Its kinda sad to rarely see anyone mention this little guy anywhere. I guess it must be because its official promo artwork and several of its in-game sprites looks horrible.. Unlike any other media, like TCG cards, the anime, stickers, etc.. Even spin offs, like PMD and pokemon XD and Colosseum got it better than the main series art ! ..they did for a while anyways.. Gen 5-6 did it some good finally !
Mightyena has a special mention, simply because of the one in the Zorua movie! (what happened in that scene was a way better interaction than what's in pokemon amie for mighty XD)
Then, Zigzagoon, Raichu, Eevee, Fennekin, Flygon, Ampharos, Lapras, Electrike, Mew, Quilava, Meowstic, Shinx, Buziel, Chikorita, Slowpoke, Minccino, Zorua, Squirtle, Nidoran, Growlithe, Breloom, Taillow, Sandile, Helioptile.. *gasp for air*
And I should stop here I think XD
Its hard to mention just one really.. :(