The Elder Scrolls IV: Oblivion and The Legend of Zelda: Majoras Mask (if it counts as a RPG). :D Both games were pretty revolutionary, in my opinion.
Oblivion because you get to make your own character (including picking your own race and skills such as being a Orc Thief, if you want to) and do whatever you want, basically (including killing everyone. ;)) Theres also loads of quests, too, and some plug-ins and expansions. :)
Majoras Mask simply because it is completely different to the ther Zelda games, story/plot wise. it's dark, sinister, scary in contrast to the others. :\ Plus, Fierce Deity link is awesome, and I love the Kafei/Anju subplot. <3