While I have no desire to see Dark Matter or Star Drive (ugh) brought back, there are a number of old TSR properties I'd like to see developed as shiny new d20 editions.
Chief among these is Gangbusters, which (I am still convinced) was the best game TSR ever published. We had an absolute riot with it.
I also wouldn't mind a d20 Boot Hill, though I doubt the viability of such a product in the marketplace. It might do okay as a one-shot stand-alone, though.
I wouldn't have minded seeing Top Secret, but agree with Joshua that Spycraft pretty much covers the genre. For the same reason, I don't see a need for a new Star Frontiers, since we now have d20 Traveller.
Of the D&D properties, I'd love to see Birthright or Al-Qadim brought back, or Mystara. Dark Sun I never much cared for, and Planescape is covered (albiet shallowly) by existing material.
The big one that I'd like to see come back as a fancy d20 game, though, is Empire of the Petal Throne. I know GOO is supposedly doing it as a Tri-Star product at some point, but that project seems to me to be floundering and I'd frankly rather see it as d20, where it would stand (IMO) a better chance in the marketplace.