1) Planescape:Torment, it never got pushed publicly like most RPGs but it could be the best PC RPG to date as far as story goes.
2) Record of the Lodoss War for Sega Dreamcast. It came out late in the DC's lifespan. But it was a great game, much better than any Midway Gauntlet game or even Bioware's Baldur's Gate Dark Alliance games.