Er... this is a hard one you know.
I'd say Half life/Half life 2 is the best one thats carried on in this generation, but not 100% sure on this.
The Metal Gear series is also one that stands out for me, though I've only played the first all the way through on the Gamecube and loved it.
The original Crash Bandicoot and Mario/sonic games (Mario All Stars especially) seemed to be the best in the last generation to me.
i bought Metal Gear Solid 2 today, knowing the PS3 plays it, so I'll play through that now. Hope to love it like the first
PS3 doesn't support Metal Gear Solid 3 yet though on the compatability list. Shame...