I'm going to second the motions for C&C, Unreal and Half-life to be remade. These are among my favourite games, but:
C&C just to have the game mechanics & graphics updated whilst keeping the original tone and feel of the cutscene-driven storyline (the whole UN-style GDI vs the charismatic & enigmatic Brotherhood of Nod, the idea of an information-driven, PR-driven war setting in a contemporary military conflict)
Unreal - mainly graphics upgrades but also to flesh out the story a bit more. I appreciate the minimalism and simplicity of the original story, but they could have added a bit more spice to thingss.
Half-life - almost purely a graphical upgrade. A game that is still so awesome, sooooo far ahead of its time that modern games still haven't caught up with aspects of it. I'd like to see even more set-pieces, but the graphics you can implement today would just make some bits which are plain "excellent" into "pure awesome".
But if anyone ever lays a hand on Grim Fandango, they're going to pull back a stump (I, ftr, never had a problem with the control interface. But if you retooled that slightly and maybe updated a couple of the character models maybe I'd just give you a verbal spray instead of the whole hand-thing...)
My $0.02