This list doesn't include action-RPG or adventure games, so I'm not making any entries from Zelda.
1) Chrono Trigger
A near-flawless game even by today's standards. Its musical score is still one of the most heavily remixed, and its characters and story work incredibly well; it basically takes every RPG cliche and figures out a way to twist it into something that's genuinely engaging. Many, many things could be said about Chrono Trigger, most of which serve to heap lavish and well-deserved praise on the head of Masato Kato. This was easily the pinnacle of SNES gaming; it just didn't get any better. Shit, it still doesn't. This game is the king of RPGs, and any other opinion is wrong. You should have seen what happened to the last guy who told me it was overrated.
I CHALLENGED HIM TO MORTAL KOMBAT.
2) Final Fantasy VII
Even non-gamers have heard of this one; it's basically the breakout RPG for the entire genre as far as America is concerned. Writers Yoshinori Kitase, Hironobu Sakaguchi, and Tetsuya Nomura stated that they were taking the series in a more sci-fi direction, with a more realistic atmosphere. Gamers at the time questioned how this was to be melded with the more fantastical elements that put the fantasy in Final Fantasy while preserving the characterization, plot, and artistry that the series is known for.
Obviously, they hadn't played Chrono Trigger. Silly rabbits.
It took off, and it remains the most popular entry in the series. It's been the cause of countless internet bitchfights about which game is better and who's hotter, and like anything popular, the source of many terrible, horrible fanfics. Seriously, I think I hate the Final Fantasy fanbase more than any other fanbase ever. But the game itself is nothing short of a goddamned masterpiece.
3) Chrono Cross
This was going to be number 2, but it has twenty damned useless extra characters that add precisely dick to the plot. Other than that, it was awesome, though there was a backlash among the Chrono Trigger fanbase for not featuring the main characters of the original in a starring role. Entire webrings have sprung up dedicated to Cross-hate, but the game's plot was actually better than Chrono Trigger's, building off of its predecessor in powerful and controversial ways. I've never understood this mentality that seems to only prefer shameless clones of the original game. Chrono Cross was new, different, and it ruled. It reached Greatest Hits status, but Final Fantasy made and continues to make more money, so we don't get any more Chrono games.
And that's terrible.
4) Final Fantasy X
The first PS2 entry into the FF series was also the first to incorporate voice actors. This was a controversial decision, but it did seem to catch on. The graphics are the best to be found on the system, and the plot is actually a lot deeper than most people give it credit for; it picked up FFVII's tone of addressing some hot-button issues, which had been all but abandoned for VIII and IX. The game is very dark and oriented more towards mature themes, which is how I like my RPGs. It's also one of the only RPGs in which the main character dies in the ending, and one of the few to prominently feature a death metal song in a soundtrack bursting at the seams with piano and hymns.
5) Diablo II
This game is also known as digital crack. It's only recently been displaced with the arrival of another helping of digital crack, World of Warcraft. Blizzard North's massive RPG keeps the same story of the original installment, but expands the game world to epic proportions, far beyond the scope of the dungeon in quiet little Tristram. The game features a story that borrows heavily from gothic fantasy and religion, while also allowing for seven character classes and thousands of items, affording for more ways to develop a character, and a fighting team, than any other RPG in existence. Blizzard also offered a great deal of support to the game, releasing no less than eleven patches for the game, each of which introduced gameplay features over and above the original.
6) Star Wars: Knights of the Old Republic
Many feel that these games are the true prequels, in the stead of the actual prequel movies. The first installment of the series was as massive in its scope as one would expect of the Star Wars galaxy, and there was no shortage of customization options. Its characters were fairly cliched, much like many of the other classic RPGs out there, but they managed to perfectly capture the feel of the old-school Star Wars, while at the same time providing a new dimension of moral thought to play around with. The only disadvantage in the game is that its morality is plagued by Jedi idealism; this issue is more than adequately addressed in the sequel.
7) The Elder Scrolls III: Morrowind
This game possesses two standout features; its beautiful musical score by composer Jeremy Soule, and its open-endedness. There's almost nothing the player can't do within the game world. Due to this, it's hailed by many as a breakthrough effort on the part of Bethesda. Despite its real-time fighting, its battle mechanics are essentially the same as those of KOTOR or Diablo, but they aren't handled nearly as well, which causes the game to lose points. It also has a lackluster graphical engine, especially where player models are concerned. But its other features are enough to save it.
8. Final Fantasy VI
This FF entry is considered by many game critics to be the best in the series. I obviously don't find this to be the case, but it doesn't change the fact that it's a fun game with some truly original content and a classic musical score. It loses steam in the second half, but not to anywhere near the extent of KOTOR II's endgame.
9) Star Wars: Knights of the Old Republic II - The Sith Lords
The sequel to the bestselling KOTOR, the game, much like Chrono Cross, featured a different cast of characters, with the original crew playing only an indirect role in the player's adventure. The stakes are substantially more dire in this game; despite eventually winning the war against Darth Malak, the Republic has been wrecked almost beyond the point of repair. The Jedi have disbanded, crime and exploitation reign supreme, and the brave souls that fought in the war have been left with nothing to return to. You play an exiled Jedi who last saw the civilized galaxy in the Mandalorian Wars. Returning to find everything he knew gone and the galaxy in shambles, he sets out to put things right. Or to exact revenge on the Jedi, if that's your cup of tea. Either way, this game makes you actually think about morality in a way that the first game didn't; on top of that, the gameplay mechanics and available options have been improved. The reason the game didn't rate higher is because of its lackluster ending; LucasArts rushed Obsidian to get the game out for a Christmas release, in the process forcing them to cut out much of the ending, including parts that would have made it more coherent, and that alone is enough to hurt it badly for these purposes. No news has yet been announced on a possible KOTOR III, but it's safe to conclude that they're going to do one, based on the numbers generated by the other two.
10) Xenogears
The game is an awful lot like a 40-hour movie, actually. But at least it's enjoyable to watch. The game's plot was done by Masato Kato, the creator of Chrono Trigger, so you know it's going to be thought-provoking. The actual battle mechanics are somewhat lackluster, save for the sections involving MOTHER FUCKING ROBOTS AND SHIT!