1. Star Ocean: The Second Story:
This was the most spectacular game I have ever played in terms of RPG elements mixed with immersed story telling. The game overall was FATHOMS deep, there was a crafting system that was at least as complete as any MMO. The dialog was well translated from the Japanese origin to provide the scope of emotion into the words, the characters REACTED with the dialog which was awesome. It was a very well done 2d-3d mesh environment similar to Final Fantasy 6 (or 3 for you freak fanboys). The random battle system was active, but not so much where you had to have knee-jerk reactions to save yourself, but it was fast enough to not get grind-heavy. The plot, OH my god the plot. Claude crashes onto a foreign planet, that later gets blown up, and winds up on a 3rd planet that he chooses to save on principal.(If memory serves, its been nearly 12 years since I played it I think) To boot, there are TWO different stories as you can start as Rene as well, and that changes the character interactions and some of the dialog choices in key-points. I liked Claude's version a lot more, but in the end its the same thing. There is that one game that touches a player, and this game was that for me.
2. Final Fantasy VIII
This was the best romance novel I have ever read lol. The love conflict between Squall and Rinoa is fantastic, emo at times, heroic at others, but badass all around. One of the deepest final fantasy character customizations I have seen. You could script your characters to be literal badasses in one specific aspect and Junction spells to strength your stats and skills. When you first get a stack of 100 quakes and you throw it on your STR and you see that number go from 102 to 275 (or was 250 the highest I cannot remember) is phenominal, having nearly max HP at level 12 learning the life refinery ability with Siren. I loved the card game too, had a save file that has over 200 hours played into it, I've unlocked everything except the UFO Easter Egg.
3. Mystical Ninja Goemon
Fuck, yes. This game was slapstick comedy wrapped in an action RPG ninja puzzle game and then it let me pilot a giant robot! HOLY CRAP! I never owned the game, I did however rent it enough from Blockbuster for my N64 that my mother probably wishes I bought it lol.
EDIT:
Honorable Mentions:
Jade Empire, World of Warcraft, God of War (franchise), Half-Life (franchise),
