We're getting really close to releasing the Beta of UQM-HD, which should hopefully fix a few of the problems posted in here. Sorry about that.
I feel like I'm in over my head when it comes to the Windows installer. I was just curious if anybody here could help us out. We've got a Mac programmer, a Linux programmer, but no Windows guy anymore.
Well, I forget what it's called, but Freeciv uses some common installer software that's free and should be good. I think it tells you when you run FreeCiv's Windows installer.
Other than that, the standard for installers in Windows is the "msi" ("MicroSoft Installer") format, and I think there are various official and unofficial tools for creating them. Try searching specifically for msi tools.