I've been using the freeware version of the jv16 Power Tools (1.4.x) for quite some time and it works great. It allows me to search the registry, do complete find/replace operations simply, scan down orphaned registry nodes or files, registry backups, etc. It doesn't do anything without asking and expects me to know how the registry works; it doesn't treat me like a simple user.
However, jv version 1.4 is getting long in the tooth and I'm not sure of its viability for Vista and Windows 7. I would upgrade, but the newer versions have switched away from the "here's a tool for someone who knows what they're doing" mindset to the "press this button to fix all your problems" mindset. I'd rather not use a program that's going to do things without my knowledge or permission. Also, I don't trust companies that say their software was the "very best registry cleaning in both performance and accuracy of the products tested in this comparison study", but the study was conducted by employees.
I was wondering if anyone else used a similar (preferably open-source) program they'd like to recommend. Or, if you have experience with the newer versions of jv16 and would like to convince me, that works too.