Wow. My library is smaller than I realized. But I can try anyway...
1. Sora (Kingdom Hearts series)
It's like SquareSoft/Square Enix decided that they wanted Peter Parker, but Final Fantasy style, so we got Sora. Kid gets strange powers, loses everything, still remains an upbeat hero. And he gets to grow up, too. He also winds up with added layers as the story progresses. It's just a lot of awesome. If Square Enix is being true to recent trends, I may even get to play KH3 without buying a Sony console.
2. Kyle Katarn (Dark Forces/Jedi Knight series)
Ancestor was a Jedi. Learns this after helping the Rebellion save the day without once using the Force. Upon learning to use the Force, takes down not just one but two enemy groups hell-bent on using the power of the Valley of the Jedi for nefarious ends. This equates with all kinds of dishing out of destruction. This story also influenced the Expanded Universe books, with Corran Horn similarly learning in a sideways fashion that he has a heritage as a Jedi. When your story influences books, you know you've got a game character to remember.
3. Joanna Dark (Perfect Dark series)
Yes, the whole thing where all the conspiracies led to aliens was a bit far-fetched. But Joanna was still the kind of kick-ass heroine that provided a counter-point to Lara Croft for as long as Rare was willing to try it.
4. Lara Croft (Tomb Raider series)
Okay, the reboot Lara may be quite different, personality-wise, from the old Lara. But at her core, Lara is still a kick-ass archaeologist that would put Indiana Jones to shame.
5. Fox McCloud (StarFox series)
Leads a completely inept team of mercenaries, manages to save his star system anyway. Repeatedly. Fun times are had by all. Except for Slippy, who everybody should slap repeatedly.
6. Commander Shephard (Mass Effect series)
Well, you can't very well leave him/her out of this, can you? Shephard is freaking awesome. Admittedly, the way he/she goes out in the end is disappointing - dooming everybody, becoming the lord of the Reapers, turning everybody in to a cyborg, or blowing up every single AI in existence aren't really happy endings - but getting there, Shephard is, no matter how you play the game, awesome sauce.
7. Yuna (Final Fantasy X games)
I know you want to call bull for me saying both games have her as a main character, but think for a second. Her father is the last summoner that managed to defeat the gigantic sea creature of doom. Yuna is the religious figure around which certain points of the first game center (for example, the burial ceremony). She is Tidus' romantic interest. The Guado prince tries to force her in to marriage. And the final battle turns out to be with all of her summoned creatures. The second game is a bit more obvious about her being the central figure, but just because you can fight without her in your party doesn't mean that she isn't a big deal in the first game.
8. Master Chief (Halo series)
He's a man of few words, who repeatedly saves humanity. Or, in the case of Reach, screws the pooch, but somehow manages to survive anyway. He is the face of the Halo franchise, and his response to crisis is best summed up in a line from a commercial for Halo 3: "I need a weapon."
9. Mario (FREAKING DUH)
He's Mario. I refuse to explain more.
10. Ezio Auditore (Assassin's Creed)
Out of all of the Assassins, Ezio is the one that players got to know the most. Well, until Revelations, where we find out what happened to Altair after the end of the first game. He is also the only one that we meet that dies completely happy and fulfilled. Well, okay, maybe Connor turns out okay, but we never actually find out.