Question: I've installed Steam do my D:\ drive, and reinstalled windows without backing up most of my files on C:\. I then installed Steam over the old directory. I can run all of the games I had installed, but there are some ties to the OS missing.
Can I repair my game installs somehow so that they get back what they're supposed to have on C:\? I don't mean savegames and settings files.

This is a general questions, but what prompted it is a problem with a mod installer. In this specific case, I want to install the [S.T.A.L.K.E.R. Clear Sky Complete mod](http://www.moddb.com/mods/clear-sky-complete/downloads/clear-sky-complete1) using the installer, but it can't locate my STALKER CS installation. I'm guessing it just checks the registry. I've got version 1.5.10 of the game, and the download page says it should support that.

Answer: 
When you install a game, Steam set up some registry keys to remember that it already did the first time installation. This step is done when you launch a game for the first time ( when is usually install DirectX and other redistributable needed).

When you reinstall Windows, both the redistributable and the registry is wiped, but since your steam is on a second drive, Steam doesn't need to re-download the games. But when you try to start the game for the first time, it will do the first time installation again, normally setting up anything needed for the game to run.
After installing steam on the C drive, maybe you should copy paste all files from the D directory to the C directory.