Deus Ex
The game is still as good as ever because the story is not anchored to its graphics. After seeing how beautiful the human models are in both the Source engine and whatever engine they are using for Mass Effect, I think updating the graphics side, remastering the voice tracks and music and adding any and all side-missions and storyline Warren Spector wanted to put in originally but couldn't, would make it an instant hit. I'd hire Greg Bear and Grant Morrison as story consultants if the original story were to be expanded. Especially on fleshing out a full version of "Jacob's Shadow", the fictional book you can read excerpts from during the game.
Dawn of War
I still play this RTS in skirmish mode. It's just so damn fun. But it's really showing it's age. More polygons, better textures, more balance...heck...it needs a whole new engine. I would happily buy it again. Especially if it came with a powerful army painter and an option to host points-based games over the internet. A sort of weird hybrid of traditional table-top rules and RTS, including having persistent online army profiles that can gain XP from online play, earning phat loot (read: Wargear), unlockable classes (Exarchs, named characters from canon) and fame.
Oh and none of this bollocks with being tied to Steam or Windows Live.
Arcanum
Again, except for some badly needed balance issues so that the majority of character stereotypes are equally effective (as opposed to becoming a mage, specializing in Force, vaporize everything = easy mode), the great story can carry it through a major graphics upgrade. I would love to see Tarrant in the Source engine, right down to Madame Lil's (*nudge, nudge* *wink, wink*). And that amazing string quartet soundtrack remastered. In fact, I'd love to bring back the old Troika crew and give all their work an upgrade.
For all games from here on out: As much support as technically possible for the mod community. Bethesda make money hand over fist from people who want to mod Fallout and Oblivion, who might never have been interested in the original games when first published.