I ran a test with captures to see whch of the three free ones actually removed more invalid entries. The first was CCleaner with the second being the registry cleanup tool seen in RegCleaner in consecutive order with Eusing.
RegCleaner immediately found items missed or passed right by with CCleaner. Eusing found even a larger number of items when running that right after RegCleaner. But RegCleaner saw more options like opening up regedit and displaying a main window for manual removal of the main keys there.
That was on XP at the time. Just run again RegCleaner followed CCleaner to find some 11 more items.
Following RegCleaner Eusing reported 194 items.
Quite a bit of difference seen with Eusing over the other two to start with. CCleaner is used for what it was intended for namely cleaning temp folders and other leftovers on the drive. Eusing finds far more each time as a registry scanner while RegCleaner still serves some purposes.
Registry Crawler had to be tried here but found to be more like RegSeeker and not having an automatic scanning cleanup tool like the others. Like CCleaner you can cleanup the IE history as well. It depends on the type of program you are looking for I guess.