Gonna be a bunch of repeats, but that's a given.
Final Fantasy VI - because character development. Seriously. How many RPG villains actually manage to destroy/take over the world, let alone be really solid characters who can be downright sympathetic at times? Love ya, Kefka.
Chrono Trigger - because beating up Gato, and the reasons it's so fucking loved.
Metal Gear Solid 3 - I could argue in this masterpiece's defense for hours, but the tl;dr is that it's feelsy as shit. MGS4 doesn't even top it in my book, and MGS4 is fucking depressing. The Boss is easily one of the most(if not THE most) well-developed, empathetic, and sympathy-inducing characters in the series, and holds a shining place in my top gaming characters list. I fucking love this game.
Legacy of Kain: Soul Reaver - This entire series (except for Blood Omen 2, ugh) is gold, AFAIC, but Soul Reaver takes the cake for installing such a deep and symbolic level of conflict and morality to an already wonderfully-developed plot. I'd put the original Blood Omen in this list, as I do feel it's a solid ten, but I'll lump it here as being the trigger for this awesome series, as well as having a plot that was ahead of its time as far as symbolism and meaning are concerned.
Romancing SaGa III - The SaGa games are hidden gems of the SNES RPG era IMO, but III is my favorite just because of how open it is. You've got so many different characters to play through and so many different choices to make, not to mention the scope and enormity of the ending (The entirety of existence being erased upon defeating the final boss, whose power of absolute destruction was magically altered to reconstruct existence after it had been erased. Duuuuuuuuuuuuude.
Mega Man X - This puppy was pretty damn perfect back in 1993, and it still can hold its own. Nothing like having near-flawlessness to boot a new timeline continuity. Oh, how Capcom has fallen.
Mega Man Zero 4 - In particular, because it really analyzes the "hero mentality" from the POV of the actual "hero" in addition to the generic bad-guy talk ("You thought you could save everyone? But wouldn't killing me make you just like me? Muahahahah, moral conundrum! Take that!"). And because gameplay's pretty damn solid.
Super Mario World and Super Mario World 2: Yoshi's Island - I don't think I really need to elaborate much. Epitomizing platforming on such large scales speaks for itself.
Devil May Cry 3 - Yeah, yeah, I know, it's a little overrated. But it really solidified the (original timeline) series' style, picking up the slack that scraps of DMC1 (and pretty much all of DMC2) left behind. The story's pretty nice, too, and the soundtrack is to fucking die for. Vergil Battle 3, I can't even.
Metal Gear 2: Solid Snake - This treasure set the tone and standard for the series' future, all years ahead of its time: "It doesn't matter who wins here. Our fight will continue. The loser will be liberated from the battlefield, and the survivor will live out the rest of his days as a soldier." Seriously. If that quote doesn't say it all, I don't know what does.
Eh, I'm tired. I'm done explaining, lol. I'm gonna list from here out.
Mega Man Zero 3
Demon's Crest
Starfox
Halo 4
Silent Hills 1, 2, and 3
Super Metroid
Final Fantasy VII: Crisis Core
Final Fantasy VII (I can defend the ever-loving SHIT out of this, but it would be a text mountain)
Quake
Legend of Dragoon (which happens to be my favorite game of all time, so biased choice is biased)
Doom & Doom 2
God of War as a whole
Medievil
I'll post more when I can think of them