Do you have a next-gen (preferably PS3) available? Ico/Shadow Of The Colossus, Metal Gear Solid 2/3, Zone Of the Enders 2, Devil May Cry series have (rather) better versions in their HD collections (ZOE2 is hardly any good on X360, though).
On the other hand, Silent Hill 2 and 3 are totally ruined on last-gen. Either the PS2 versions, or PC (some of the effects aren't that good as the console originals IIRC, but they probably have some redeeming features. There's a megathread about the PC versions on NeoGAF - might be worth checking out).
Also, Yakuza 1 and 2.
Of course, I don't know whether any of them is emulated any well.