I usually just use MS's stock tool, but I did one time see a third-party program that had a lot of advanced features, like searching via regular expressions. It didn't work with x64 at the time, though (late 2005) ... I wish I remember what it was called.
For the most part though, I would be a little hesitant to trust a third-party to manage my registry.
Yeah, I looked some up but wanted to check if anyone else had some experience with them. My main gripe is that it takes forever for a key to be found if I copy in a search, and it really shouldn't. Last night Silverlight didn't want to install correctly and it was because some permissions were f**ked up on the registries it was wanting to overwrite. I ended up having to find them all individually through the tree because it really would have taken longer for the search to complete - I've waited a full minute before without my result popping up, even though I was trying to navigate to a specific key.
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You might already be aware of this, but for generic searches, it starts searching in your presently selected key, and works downwards from there (without wrapping).
So if you have the Computer node selected, it will search the entire tree, but if you know what you want is in HKLM, just select that and search. And unless you want something that you know is in HKCR, just skip it and select HKCU -- since HKCR is so damned big, you can easily spend half of your search-time just parsing through it.