If you look under HKCU, it's (obviously) for whomever you are logged in as, I always look under..
HLKM/Software/Microsoft/Windows/CurrentVersion/Run
Also, uninstall info is under...
HLKM/Software/Microsoft/Windows/CurrentVersion/uninstall
what I do (which is what msconfig would do) is create a folder named Run-, and copy all the keys I don't want in Run to Run-, so that the keys are still here and easily accessible, incase something you take out breaks something..
-Jason