Genso Suikoden II: While most JRPG heroes seem to fall underneath the two categories of "Invulnerable, unfeeling, killing machine" (See Crono of Chrono Trigger), or "whiny, emo-wrist-slitting, ball of putty" (See Squall Leonhart from Final Fantasy VIII), or a combination of both (See Cloud Strife from Final Fantasy VII), Suikoden II introduces a character who seems to balance both emotion and general harbinger of doom pretty well. One of the few (questionably?) homosexual RPG heroes, "Riou" (at least according to the novel), a young lad at about 16, has to rally a nation to defeat his homeland which betrayed him, which ends up being lead by his best friend/lover(?). The only reason I keep questioning the hero's sexuality is simply because the game continues to have the two give each other longing looks, as well as the song that plays when they're in the same screen (Reminiscence) had been commissioned by Konami to be turned into not one, but two love songs. 108+ characters to keep track of, but the amount of diversity between them don't make them that hard to keep track of. Also unlike later games in the series, you don't have to (as in plot line forces you), to make decisions that make no sense, such as recruit a paedophile in your ranks.
The first play through seems to actually have some twists and turns and there are multiple endings, none of which seem to be simply "All is right and beautiful in the world" which is how ordeals usually end up. Finally, back to the hero, while most games do attempt for the "Silent Protagonist" angle, so that the player feels like they somehow are talking (I've never really understood that), the dialogue in the game comes off that at least Riou is speaking and people are responding to him. No inane or random verbiage like one sees in early Dragon's Quest games, or the ilk, but rather what sounds like the second half of a conversation, while confusing at times, it does make the "Silent Protagonist" angle a bit easier to swallow. Also the setting of some fantastic rendition of China makes the game less cookie cutter from the majority of RPGs that generally set the characters in a pseudo European Medieval environment or Feudal Japan.
Fallout 2: Wonderful story simply because there is no real set plot. You are dropped off in the middle of the apocalyptic desert that once was the northern west coast of the United States, and your story depends on what you do where. People don't seem to be simply sitting around waiting for some hero to complete their day, and while the events are scripted to not occur until you arrive, the events seem fresh enough that they have the odour of "just happening." Companions and allies alike have personalities that make them enjoyable to interact with, making your story of the Chosen One as unique as the player and their character. For those of you waiting for that Mad Max game, this would be it.
Chrono Cross: One thing that seemed to be dreadfully missing from the first game, Chrono Trigger, was the fact that one should have been spending more time messing with the very fabrics of the space-time continuum. Every time frame seemed to simply be independent of one another aside from subtle differences, and when one actually does get the chance to do something, it seems like your efforts didn't do much (in example, after turning a desert into a forest, the adjoining town seems exactly the same). The third instalment of the Chrono saga (counting Radical Dreamers), sates that thirst for wanton misuse of power, even if it is simply in parallel universes. Again, like Suikoden, the cast of characters is immense, but it isn't difficult to differentiate a Mexican luchador exorcist from someone with an annoying faux Australian accent. And speaking of messing with the space-time continuum:
Day of the Tentacle: A masterful reminder that Tom Schafer was one of the two golden boys that LucasArts proceeded to treat like faeces and shoo them off. The game takes place once again in the evil mansion owned by that strange Edison family, but this time in the past, present, and future. Getting to interact with Schafer inspired Founding Fathers (which would put the Edison Mansion somewhere in the East coast, (which would put the mansion somewhere near Philadelphia) is pure comic genius. The static cast of heroes (unlike the group of teens you could chose from in the original) were exceptionally well rounded and made the player think about how to interact in different situations, which created a complex story of doing the same action without being repetitive.
Ninja Gaiden/Ninja Gaiden II: Dark Sword of Chaos/Ninja Gaiden III: The Ancient Ship of Doom: One of the first games to utilize the "Cinema Sequence" that is commonplace in almost all games today to push along a storyline, The Ninja Gaiden trilogy gains a sentimental place on this list. Not as ground breaking, or as deep as some of the other games, it was interesting to see a platformer have something more than simply "Run right" as it's whole point.