There are truly too many underused Pokemon to name, in my opinion (and from personal experience of not using Pokemon), but dividing them into a few groups...
Starters: Almost all grass starters are underused (perhaps with the exception of Treecko). Everyone I know goes for the Charmander or Totodile, leaving no love for the poor Bulbasaur (though playing through G/S/C, I just get Chikorita for the low level Razor Leaf to breed to other grass types XD).
Single evolutions: Almost all of them, I don't know many Pokemon (besides legendaries and odd-balls like Wobbufett) that don't evolve that are commonly used. Mostly due to the wide variety of moves and strength that comes with a fully evolved brute, not to mention a feeling of progression and development as your Pokemon grow in the game.
Types: General types I see almost no one use is Fighting and Poison (and when used, mostly for their other type and not for one of those two). During the game course, they usually aren't seen as necessary staples on a team to progress (their type advantages shared by other types that don't share the Psychic weakness). Also, pure flying types are never used. XD
Legendaries: Articuno, in my opinion, is the least used legendary, excluding those only gotten from Nintendo events, for obvious reasons. I'm not sure why exactly, but I do remember everyone flocking to Zapdos in RBY days (unintended pun).