InformationWeek has a great article comparing ten Windows Registry Cleaning software titles. They tested each title on an identical disk configuration.
I made a disk "image" (a bit-for-bit exact copy of the hard drive's contents) and then tried the 10 different Registry cleaners on the test system, one at a time. First, I'd install and run one cleaner three times, with a reboot between each run. I'd make a note of the number of Registry errors the software found and fixed on each run.
Author Fred Langa reports that EasyCleaner swept the free class and JV16 PowerTools 2005 was the best commercial tool.
Registry Cleaning Software [InformationWeek]