I'd say some of the funniest Pokemon are:
-Skitty, because it has that cute meow and look, and funny expressions... plus that weird way of chasing its tail and bumping into things...
-Victreebel/Cacnea, because when James sends them into battle, they attack him first...
-Torchic, because of the way it tried to get that Bluk Berry in one episode and the way it ran across some rocks and crashed into another rock...
-Psyduck, because of its affairs with Misty and the way it battles...
-Slowpoke, because of its personality...
-Snorlax, because of its eating habits.
-Wurmple, also because of its eating habits.
-Muk, because of the way it "hugs" Professor Oak.
-Lotad, because of its weird personality and battle style.
I'm sure there are others too...