What a great topic for my first post here. Of games that were at least rumored to have been worked on:
Colonial Conquest (SSI, easily #1)
Buck Rogers: Matrix Cubed (SSI)
Shiloh: Grant's Trial in the West (SSI)
Sons of Liberty (SSI)
Of games that weren't even rumored, I still would have love to have seen good conversions of SSI's Rails West!, Imperium Galactum, and Geopolitique 1990...actually the entire SSI catalog would've been good. Also, never released on any platform: the third game in SSI's Roadwar 2000 trilogy and the third game in Sierra's Manhunter trilogy.