I am a
raging Shin Megami Tensei fan (Hah, I forgot that one word is filtered here). It contains my new favorite game of all time, Persona 3, while the rest come right behind it and share such high spots with Deus Ex and the like.
Onimusha: Dawn of Dreams. I love the entire Onimusha series, but I believe the fourth game to be the best of the bunch. It's almost funny, because it's largely considered to be the weakest installment by most other fans (At least from what I've seen).
Deus Ex. Obviously. I'd deserve a good pistol whipping if I didn't mention it in a favorite game topic. Twice.
Morrowind, again for obvious reasons.
Shadow of the Colossus. The perfect blend of a great story, great gameplay, and awe-inspiring artistic eye candy.
Valkyrie Profile 2. Just recently discovered this gem. I feel like an idiot for not having played it until now. Perhaps even more visually impressive than Colossus, but that's just my opinion.
Ninja Gaiden. I like both modern installments, but the first will always be my favorite. However, from what I've seen, Sigma 2 fixes all of my issues with the second game (Less enemies onscreen, less projectile spam, better performance, more unlockables,
a cooperative Mission Mode).
Devil May Cry. Excellent series. Didn't like Nero stealing Dante's spotlight in 4, but I still liked it. Too bad Capcom decided they couldn't be arsed to develop the next game and handed the workload over to Ninja Theory. Oh, how I
hate Capcom this gen.
Silent Hill series, specifically 1, 2, 3 and 4. I don't like what I see with the new installments, and the one coming out looks like a bland piece of [censored]. Still, I love the better half of the series. I will admit the gameplay svcks across the board, but I play Silent Hill for total immersion into an isolated and creepy environment (as well as its plots), not for its gameplay.
A good chunk of the Final Fantasy series. I have played and liked 6, 7, 9, 10, 10-2 (Yes, it's possible to like all of those AND 10-2) and 12. I absolutely despise 8, so don't bother asking me why I skipped over it.
Chrono Cross and Chrono Trigger. I believe both games are equally amazing. Both of them have incredible stories, fantastic musical scores, likable characters and killer combat systems. What's not to love? For me, nothing.
Tales of Vesperia. IMO, the greatest JRPG of this generation. Problem is, I hate Namco with a fiery passion because they insist on keeping the better half of the Tales series in Japan and forces us to wait a decade for a localization or import it and either learn Japanese or use a tedious translation guide. And yes, I'm aware there's a localized 360 release. Too bad that's a half finished game compared to the PS3 version the Japanese are enjoying.
Donkey Kong Country 2. Greatest. Platformer. Ever. Also, best soundtrack to a platformer ever. I can't think of a single flaw this game contains, other than the fact that it ends.
Moved to the main list. I don't know why I put this in honorable mentions.Honorable mentions:Medal of Honor: Frontline. Loved this game when I was younger, would still love playing it again. IMO, the best MoH.
Knights of the Old Republic. I don't like Star Wars at all, yet this game was still incredible to me. Yeah, it's not one of my all-time favorites. "Heresy! Burn him!" and all that jazz.

Baldur's Gate. One of the most impressively deep D&D games I've ever played. I can't believe how much content is packed into that game.
Planescape: Torment. I came very close to listing this as one of my main favorites, and while I absolutely loved the plot, it just didn't give me that fuzzy feeling that the above games do. Still, I don't think I've encountered quite a story like it.
The Soul Calibur series. Only fighting game series I give a damn about, both because I prefer weapons and because it's newbie friendly. You can keep your overly technical Street Fighter and Tekken.
Grand Theft Auto 4. I believe this to be the best GTA yet. I, for one, never enjoyed the mind-numbingly tedious and annoyingly difficult minigames of Vice City and San Andreas, and I do not miss them in the
slightest. I like the new physics, I think the cell phone system is pretty cool, and the graphics upgrade was very nice. So yeah, unless you haven't figured it out by now, I'd prefer it if GTA continued with the realistic approach rather than the cartoony one of previous entries.
Moved to honorable mentions list.Roller Coaster Tycoon 3. Fantastic visuals, tons of customization, insanely good performance (One of the few good-looking games my crappy PC can max out), and the ability to view the parks at any angle, even in first person view in any ride. Holy hell, it's just too much fun.
Sim City 3000. I like 4, but that game has a lot of issues, especially in performance. I have such fond memories of 3000, being my first coop experience (I played it all the time with my sister), and the soundtrack is just great. It may not have the depth of 4, but it certainly has more charm to it.
Odin Sphere. It's hard to describe just how much of an experience this game is, but it certainly is a damn good one. Visuals that look like a moving painting, fast-paced visceral action, RPG elements, and a surprisingly involved story with a good performance from the VA cast.
Fallout 3. While I didn't totally love the game, I cannot deny that it's one of Beth's greatest achievements of all time, and is one
hell of a good post-apocalyptic Action RPG.
Lost Odyssey. A good effort by Final Fantasy's former main man. Extremely emotional with an excellent score my Nobuo Uematsu and good gameplay. However, Disc 3 was just awfully tedious and the story kept getting worse. Otherwise, it wouldn't just be an honorable mention.
I'm sure I've missed a lot, but I think this has gone on long enough.