For me it is The Saboteur. I understand the faults for it but the story, music, and style were amazing.
I guess another one would be Dark Sector, it was a thrill ride and I often ask my self why its like 5 bucks.
Hyperdimension Neptuna. I have been playing it for less than an hour but I'm already starting to like characters and music.
Super Robot Taisen Saga: Endless Frontier why was this never as appreciated? I LOVED the fighting system and the interactions with the characters.
X-Men Wolverines: Origins. One movie tied game that I was able look past its flaws because the ride was pretty fun.
Castlevania: Circle of the Moon. This was my very first GBA game and I guess it came and went because the overall game was EXTREMELY dark and I couldn't see anything with the standard GBA.
Marble Blast Ultra. A game that I can literally take 30 min to beat ONE level and have an awesome time with.
Dino Crisis. Why wasnt this game as popuas RE2? It used a lot of the same mechanics and was extremely suspenseful. A very complicated game but in a satisfying way. To this day I cannot beat.
Rival Schools. Capcom bring this series back! I miss Batsu! I loved this game to death and found it extremely fun. Remake this game or put it to HD!
Sonic Adventure. For what it's worth, I have the best memeries with this game as a child.
Jet Set Radio series. They merely came and went. I'm super happy for the HD remake, as long as they include the music I am fine!
Zombie Revenge. Oh my God did I have the greatest time with this game! Re-release it and take all my money!
Duke Nukem. I cant remember which ones these were but the ones where it seemed very 8-bit. Before Duke had glasses. I played these on the PC and had an amazing time with them as a child.
Have plenty more but I'll save my fingers...