Soooo many I'd like to see, a lot of which have already been mentioned.
Since I'm currently playing through one of their games, I'll just say I'd love Troika's unfortunately small catalog redone with modern tech (i.e. VTM:B on the latest Source version, and maybe Arcanum/ToEE on a modified Diablo 3 engine) and all the unfinished/cut/poorly implemented content for each properly realised. Yeah, the respective modding communities have done great jobs, but...ah well...