Based on my experience with each of these registry cleaners, I've put the better choices at the top of the list. Most of the others are abandonware and haven't been improved, but they still work!

CCleaner is the best free registry cleaner I've tested. It's easy to use, prompts you to back up the registry before making changes, and includes a number of other useful tools.

Piriform offers both installable and portable versions of their free registry cleaner.

If you want to use an automated tool to fix a problem caused by a registry issue, I highly recommend using Piriform's free registry cleaner CCleaner.