Registry Mechanic Registry Cleaner
Registry Mechanic is a registry cleaner that has a nominally free version (but you're really going to have to pay to get it to completely clear out your registry). People who have tested it have found a pretty dramatic reduction in the time it takes to boot up your computer.
The first thing it does is scan your registry. You can do this for free, to see in advance what problems you're going to deal with before you pay. You can see below that Registry Mechanic scans through a bunch of different sections, including a deep scan that will catch a lot of stuff other programs might not.
There's really not much too it - you don't have to be a computer geek to be able to figure out what to do. You just click the repair button, and it will run through all the fixes. If you've gone with the free version, you can get a partial fix, but not a complete one. Still, on my computer I was able to fix about half the errors without even having to pay a penny. Granted, this was a newer computer without that many problems built up yet.
There are also a few extra features - it can scan the hard drive for malfunctioning shortcuts (for example, if you've deleted something and still have lingering icons on your desktop). You can set it to automatically scan your registry whenever the computer starts up, if you're worried about a recurring problem. It also has an "Ignore List" that will let you set certain items as off-limits for any future scans.
Useful Links:
http://www.pctools.com/registry-mechanic/rmlopb/
http://www.whatsabyte.com/P1/registry_mechanic.htm
http://www.pcmag.com/article2/0,2817,1585475,00.asp
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