Guitar Hero - Have to say that I love the second GH the most. I've played it a lot more then the other two that I have.
Silent Hill - Silent Hill 2 is definitely my favorite, I've beaten it 10 times, usually tried to get all the endings. Got all except the 10 star rating which is a BITCH to try to get unless I were to have a lot of time on my hands to play it….
Rival Schools - the first one on PS, lol. I could never get enough of that game... (kinda miss it lol)
Soul Calibur - The first one, because I pretty much mastered it when I used to play my Dreamcast all the time....
Star Fox - the SNES one, its so awesome still to this day! Oh, the pixels XD
Donkey Kong - I really liked the first one, but I love the second one more for some reason... The levels were really fun!
Capcom vs SNK - Definitely the second one! I tend to like sequels in games, and this is no exception.
Crash Bandicoot - I really loved the 2nd and 3rd games, though I actually beat the 3rd game since I had it for a while.
Tomb Raider - Number 2 was my favorite, I still haven't beaten it... maybe I should get around to it someday, lol
Resident Evil - Again, number 2 is the best one for me. Its so epic....
Metroid - My favorite has to be Fusion because I've beaten it with a really good time. Also, Super Metroid ftw because it is just amazing.
Mario - Mario 3 on NES is still to this day one of the best. Also, Super Mario World was really fun too!
Mega Man - I think the one I beat was X5, that one was pretty fun.
Lord of the Rings - Two Towers was really fun, I don't think I've ever beaten it because I always wind up forgetting... I don't think I have it anymore though
DDR - Konamix was always my favorite, it has tons of great old songs, and I loved Ultramix 2, it had really awesome songs as well!