1. Solid Snake (Metal Gear Solid Series)
2. Barrett Wallace (FF VII)
4. Marcello (Dragon Quest VIII)
I chose this character because, unlike the typical rebel, Marcello is actually part of the ruling class. Marcello makes a bold move near the end of the game to use his position of power to attempt to overthrow the oppressing monarchy rather than enjoy the comforts of his reign. Technically he is a bad guy in the game, but that doesn't make his intentions any less noble.
There are plenty of other notable rebels in gaming I'm sure, but the few others I could come up with had many similar attributes as those I mentioned here. Still, it would be awesome if you guys thought up some more!