Windows registries will always be a mess, no questions asked. If you want a relatively unjumbled registry, constantly reinstall of go back to a super-early restore point, ghost a fresh install, whatever.
The issue isn't really the registry though. Gone are the days of having to muddle through the reg since some program changed your home page and wont let you change it back.
If you're having problems, I find that a useful combination is hijackthis and killbox. Both can easily be found on google. If it's over your head, feel free to send me the hijack this log and I'll let you know what's wrong. If you think you can handle it- it's easier than it looks.
Run hijackthis, tell it to do a scan with a log, google "hijackthis parser," paste the log in and look at the break down. There are some things hijackthis wont be able to clean up, that's what killbox is for.
Of course, having and running anti-malware software before this is always a good idea as it leaves you with less manual work.
That do it for ya? If you're looking for some specific feature let me know and I'll see if I have what you're looking for.