Honorable mentions of my own go to:
- Paper Mario: The Thousand Year Door (it's a perfection of Paper Mario, which is itself a refinement of Super Mario RPG - all three are great games)
- Super Metroid (excellently-crafted and wonderfully atmospheric, but thanks mostly to the brilliant lore scans I prefer Prime)
- Silent Hill: Shattered Memories (it is one of the best examples of interactive storytelling I have EVER seen, but the game in general is just a couple layers of polish away from true greatness)
- Final Fantasy VII and, to a slightly lesser extent, VI (I would love 'em more, but... those random battles... X was pretty good too, until roughly the last third of the game)
- Final Fantasy Tactics and Tactics Advance (Both great in their own ways, though the chore of character-building in Tactics and pushover difficulty level in Tactics Advance are the respective Achilles' heels of each game)
- The Legend of Zelda: The Wind Waker (The visual style was amazing, the story was powerful and the experience of exploring the high seas was totally unforgettable; the tedious, mandatory Triforce hunt and the fact that it's just a little too similar to OoT keep it from surpassing its predecessor, though)
- Metal Gear Solid and MGS2 (Choosing just one for a top-10 list was hard; MGS1 has the most originality and balance, while MGS2 has comparatively weak level and boss design and a story that fluctuates wildly in quality, but the ending is so damn brilliant it very nearly single-handedly puts the game on my list; MGS3, however, has the least engaging story of the bunch, but absolutely enthralling gameplay that I can come back to again and again, hence my final choice)
- The Darkness (Maybe not one of my all-time favorites, and massively flawed for sure, but I really liked it nonetheless)
