I'm disappointed in like half these answers. What about the Ye Olde heroes of lore! (i mean like NES, SNES, sega genesis, etc)
Oh and Magnus Gallant from Ogre Battle 64 is probably one of them. Probably one of the worse characters during the beginning the game, but ending up to be the 5th best. And i think that he is a hero that actually wants to do what he is doing. Unlike the John McClane syndrome most other heroes have. (Wrong place in wrong time [Har Gordon Freeman], ending up leading the rebellion or some shit)
If you want a silent protagonist from me, BOWIE from Shining Force 2. Only says 6 words the entire game, and only has his face pop up on a chat bubble 7 times (those 6 words are in 1 sentence.) One of the few characters that actually gets ?? attack with a level 20 promotion