Non-ordered list:
Chrono Trigger - still the best combination of story, characters, and battle system of any JRPG. Throw in great 2D visuals and a fantastic soundtrack, and this will probably be my favorite JRPG for eternity.
Final Fantasy VI - just about everything CT did well, FFVI did as well. But while I think FFVI had the superior soundtrack, in terms of everything else, for how good FFVI is, CT was just a little bit better.
Final Fantasy Tactics - objectively speaking, Tactics Ogre is arguably the better and more important game in the genre, and NIS has since then taken the formula to new (and ridiculous) levels, but FFT remains my favorite of the grid/hex-based strategy/tactical RPGs. The game is far from being without faults (laughably uneven difficulty, terribad localization in the PS1 version, just to mention a few), but the story and characters give the game a charm that few others match.
Valkyria Chronicles - arguably the biggest step forward in SRPG/TRPG gameplay since the genre was invented. Story and characters are not anything particularly new or inventive, but the battle system, watercolor-esque visuals, stirring soundtrack, and generally amazing presentation more than make up for it.
Xenogears - almost certainly the most flawed game on my list, but probably the one I feel most strongly about. The story may be convoluted, and localization comes from the "bad days" of Square's NA efforts, but I can't think of another RPG that I've felt so much emotion for the cast (even the non-major characters) - Citan, Fei, Elly, and Emeralda would all be on the shortlist of my favorite characters in gaming, and Id is at the top for villains.
Star Wars: Knights of the Old Republic - delivered almost everything I could have ever wanted out of a Star Wars RPG in spectacular fashion. The story, setting, and characters are all very well done (HK-47 is one of the most memorable characters in a videogame ever), and the gameplay felt fast-paced and action-oriented enough despite, at it's core, still being a D&D roll-based system.
Legend of Zelda: Ocarina of Time - is there anything left to say about this game that hasn't been said countless times before? Sure, the story is simply and straightforward in true Nintendo fashion, but the time travel mechanic, the expansive overworld, the horseriding/fishing minigames, and the combination of a camera and Z-Targetting that was 3D gaming done right all added up to one of the most memorable gaming experiences ever, evem if's it's RPG-lite.
World of WarCraft - well, there really isn't much to say about this, is there? It's hard to judge because the game has evolved so much, but even as someone who's quit the game over a year ago, it's still hard to argue against this being one of the best, and certainly one of the most important, games ever. There have always been issues in the game (the evolution of PvP certainly comes to mind), but looking back, from saving up enough gold to buy the first mount to stepping foot into Molten Core for the first time to killing C'Thun to taking flight on a flying mount, the game is chock full of fantastic experiences.
Baldur's Gate 2 - there are not enough words I can write to properly describe a game of this epic proportions. But the fact that a decade later it's still considered the definitive fantasy/D&D RPG really says it all.
Dragon Age: Origins - it's like Baldur's Gate updated for the 21st century and crossed with WoW. I had my doubts regarding this game, but 150+ hours of playing later, suffice to say they have been allayed. While it's not the prettiest, deepest, or most epic of BioWare's games, it comes together in a fantastic package that I thoroughly enjoyed.
