When running the registry cleaner and examining the found faulty entries unchecking (dubious) bad entries will add these to the ignore list, and not show up at the next run. Reg Cleaner ver. 5 used for six years on a XP computer have for me been of value keeping it very responsive (regular disk image backup plus a boot CD also have helped).
With Reg Cleaner 7.2 on a Vista laptop I just deleted > 2000 registry entries unticking (or adding to the ignore list) 20, without problems. License keys of hard protected apps. (Vegas Movie Studio etc.) are easily lost, where the undo changes center (just tested) works OK.
To me it appear this cleaner plus regular disk image backups maintain the operating system very well.