Notice: Not Top 5, just give 5 of your favorite.
My favorite are probably (1) Mega Man X (SNES/PSP), (2) Beyond Good & Evil (XB/PS2/GC), (3)Psi-ops: The Mindgate Conspiracies (XB/PS2/GC), (4)Dead or Alive 3 (Japanese Version, XB), and (5)Fatal Frame III: The Tormented (PS2).
I found Mega Man X to be one of my favorite Mega Mans, I played that game so much I actually have been close to beating the speed-run by 5 minutes. The storyline was great as well as the enhances to the Mega Man series: armor collecting, character designs (more adult), and stage designs forcing you to come back to certain levels. You also couldn't forget about using Ryu's Hadoken
Beyond Good & Evil was a really good game. I enjoyed the art design, the polished graphics, the storyline, the music, and all the characters. I don't know why it didn't sell well, probably due to bad marketing and/or mainstream don't want to be playing as a female freelance journalist.
Psi-Ops: The Mindgate Conspiracies I had a lot of fun playing with the physics. You could move anything not "nailed" down. Levitate an enemy and pump him full of lead. Levitate him and throw him into a furnace. Levitate any object and send it crashing into an enemy. You also had the ghost mode to go through locked doors and possess enemies to take out their own comrades. The saddest part is the cliffhanger ending. Where they expected this game to sell so well they were going to continue the story with a movie and then the sequel to the movie be a game. Guess it just goes to show, don't plan on your game succeeding. I don't think anyone knows the exact reason as to why this game didn't sell like hotcakes. It was marketed a lot when it came out. I do know there is one game-breaking glitch at the 3rd to last boss where the nitrogen tanks don't appear to take her out.
Dead or Alive 3 (Japanese Version). Also called DOA3.1. This game was the first time in a long while that I felt DOA had a breath of fresh air. It had many things that I enjoyed from other fighting games as well as putting them into my favorite fighting game series. You had to know your characters and your opponent's character in order to survive in that game. With the addition of frame advantage and an actual side-stepping system I fell in love with it. It's still the best music track I have experienced in the DOA series. DOA4 came out and went a different way than DOA3 so I'm not too into that. Sadly, DOA3.1 had Hayate's Cartwheel avoid nearly everything due to the Sidestep system, but was fixed in the European Version (3.2) with the negative affect of nerfing the sidestep system at the same time. DOA3 will always have a place in my heart and it saddens me that I won't be able to get that game play experience in future installments.
Fatal Frame III: The Tormented. I enjoyed the hell out of the entire Fatal Frame series. The biggest reason this isn't picked up is because "you fight ghosts with a camera?!". Mainstream want guns and explosions, simple as that. But since guns and explosions are really missing (and really won't work on ghosts, just zombies) the team Project Zero do a good job with atmosphere and ambiance. There are times when I didn't want to run in fear of a ghost attacking me. The camera experience provides a great balance to gameplay. You see, you have to focus in on the ghost, who's telporting around and trying to attack you. You can't treat the camera like a gun and pick off shots from a distance. You are rewarded for more damage the longer you have the ghost in your lens vision. Also you are rewarded with the "Fatal Frame Shot" at the moment they are attacking you. This gives you a dual-experience. You won't survive and you'll waste film just picking off shots. You're rewarded for waiting for THE moment the ghost jumps you. Bringing that sense of tension in every battle, trying not to pull the shutter while wanting to pull the shutter. I really enjoy the whole series but III took the best from II and I. But you need to play I and II in order to get the full experience of III.