1. Shemnue:
It's been my favourite game ever since I heard about it. At the time it just seemed so different and was a brilliant amalgamation of different genres. It's also got that tragedy of not being completed about it. Like the musician who dies and you wonder what could have been.
2. Hitman 2: Silent Assassin:
Again it offers you a lot of choice in what to do and can be fun on so many levels. If you want to roleplay the superhuman assassin you can. If you want to just go all guns blazing you can. If you want to dress as a postman and beat people to death with a golf club you can.
3. Metal Gear Solid 2:
My favourite of the series, mainly because its the one I've had the most fun replaying. Yes, it's painfully short and Snake is absent for a lot of it but as a game I've found it the most enjoyable and interesting of the series.
4. Final Fantasy VIII:
Another that's my favourite of the series, even if VII and IX run it close VIII has always had a place in my heart. I can remember to joy of rooting through my mums drawers in order to find it before Christmas. Seems to get a lot of hate nowadays, for some baffling reason. I love the story, I love most of the characters, I love Triple Triad and all the little side quests.
5. SSX3:
I've got to put this in ahead of things like Morrowind, San Andreas, Age of Empires because a few years ago whilst replaying I realised that I've played few games for such a period of time and loved every second of them. The characters are great, customising them is brilliant, the challenges have a nice difficulty curve to them and the courses are just insanely fun. Maybe it should be higher but I suppose FFVIII/MGS2 have others in the series to prop them up with.