ccleaner also has an "add/remove programs" function. Obviously the first thing is to look for uninstallers for any programs you want to uninstall. Most programs have an uninstaller with them. The Windows add/remove program heuristics they use to determine frequency of use etc. do tend to slow things down a bit, but failing to appear at all is slightly more worrying.
I'll have a look around and see what I can find from some of my more knowledgable friends.
As a first step, you could try opening the "run" command box and typing in "REGSVR32 APPWIZ.CPL" (without the inverted commas). This should re-register the applet and has been known to sort the problem.
Let me know if that works, if not there are a few other tricks to try. How do you feel about Registry editing?