For me first is JP SNES, first JP game I played and I played it several times. Only beat it twice though. The thing that annoyed me was that when I would play with my cousins, they would push Grant against the giant JP logos in the walls and glitch through them, causing the game to hang.
Second would be Trespasser, which should be obvious since I'm an admin at the Trespasser Community
I think the main problem of Trespasser is that they were trying to do Crysis in 1998 at a time when people were still figuring out how to do outdoor levels in the first place. A Trespasser remake in Crysis would be awesome, IMHO.
And Third would be Operation Genesis, mainly because I used to play Zoo Tycoon a lot when I was younger and an officially licensed JP version was an awesome idea (Though I do have the Dinosaur Park expansion for ZT, haha). Never could get a rating higher than 3 stars though.