Hi,
I'd recommend staying reluctant. The only registry cleaner I use is RegClean 4.1a. Yup, that sorry little unsupported Microsoft utility. It's true that it doesn't do much. It also doesn't ransack the registry and leave you with a steaming pile of duck noonie instead of an operating system.
If you're running NT 4.0, Win2K or WinXP I would recommend staying away from third party auto registry cleaners. I do use InCtrl5 (a PC Magazine utility) to monitor installation processes. I set it to record every addition to the file complement and every registry and configuration file edit made by any installation procedure. If I need to reverse registry changes, I do so manually.
I also use a defragger (O&O Pro) that defrags the registry files, the MFT and the metadata at boot time. And I use RegCompact to reduce registry file sizes. I haven't seen any performance degradation over time with my Win2K and WinXP boxes, though of course the XP boxes haven't been running for a lot of time.
If you're interested, InCtrl5 can be found in the PC Magazine utilities archives. (Ugh! They really need to reorganize that site.) RegCompact is donationware available
here.
My $.02. If registry editing is worth doing, it's worth doing right. And that means manually. There's not much we can do about the automatic registry editing that gets done by installation and uninstallation routines. But I think that using the third party stuff is just asking for it on the chin.
Hope you find a routine and / or software that suits your purposes.
Regards,
Jim