I love seeing this thread! There are so many hidden gems in the gaming community (and if anybody wants to know what the most underrated system of all time is, just buy a PSP-2000). I'm getting nostalgia-shell shock just seeing some of these titles again. I'm going to freestyle some contributions:
This is one of my favorite RPGs of all time. The amount of content in Tales of Destiny II separates it from all other RPGs of its time. Along with a 3-disc storyline and anime-esque cutscenes, this game packs an awesome 2D battle system that allows you to play with 3 other people (one of the only RPGs I know of that allows intuitive multiplayer). I highly recommend it and if you don't have a PS1, there's a PSP remake called 'Tales of Eternia'.
Honorable mentions: The Last Story, Xenoblade Chronicles, The Legend of Zelda: Link's Awakening DX
A 3D fighting game that incorporates strategy, Psychic Force 2012 is a gem. I can say that to play this game expertly requires a steep learning curve because there are so many advanced controls. The battle system allows you to fly around in a cube/sphere and chain together projectiles and melee combos. As you take damage, your 'special bar' increases, so the health and energy is intertwined in a unique way. Another underrated game.
Honorable mentions: Battle Arena Toshinden, Sonic the Fighters, Gundam Battle Assault 2
This one is interesting because it isn't a very pretty game but it is highly addicting once you get the hang of its mechanics. It combines dungeon crawling RPG elements with RTS which allows a lot of optimization. Its different from other RTS games because of the stage creation and customization mechanic. Not the best RTS but it is pretty fun.
Honorable mentions: Tactics Ogre/Ogre Battle 64, Yggdra Union
Now this one is probably my favorite on the list. There have been a TON of Dragon Ball Z games, no doubt. But I've realized that in general with gaming, some of the best and most underrated games come out at the end of a console's lifespan, which is the case with Dragon Ball Z: Legendary Super Warriors. It came out around the same time that GBA games were hitting their stride (Legacy of Goku 1/2/3, Supersonic Warriors, etc.). This game is unique however not only because of the card-based battle system (similar to Kingdom Hearts: Chain of Memories) but also because of the character roster being so big. It has one of the biggest character rosters of any DBZ game and quite a lot of replay value. Another highly recommended gem.
Honorable mentions: Yu-Gi-Oh: Dark Duel Stories/Forbidden Memories