I'm going to stump for Butterfree. In the anime Butterfree caught on early (just as it tends to do in the games), but very early on Butterfree left, not sticking around to be part of Ash's entourage.
I think the anime has a huge effect on dictating the popularity of Pokemon; Charizard was the only of Ash's starters to fully evolve and it is easily the most popular of all evolution starters.
I think had Butterfree stuck around longer in the anime, it would be more popular. What's not to love? It's a butterfly (girl appeal), has like four different move types it can learn (game appeal) and is all around cool (cool appeal).
[they didn't even make a Butterfree ex... >.< ]