I can understand not wanting to use a registry cleaner, many feel the same about defraggers. I follow the arguments on both sides and would say that you have to decide for yourself, and results may vary. All I know is from personal experience, I use both regularly and always have the fastest, cleanest running computer in the office and among family and friends, so no science, just opinion (though it could just be that I am really careful about researching what I install and run in the first place). To answer this question specifically I like to use both
RegSeeker http://www.hoverdesk.net/freeware.htm
and
CCleaner http://www.piriform.com/ccleaner
With either I suggest taking it easy, looking at exactly what it wants to do, and making sure you agree, at least until you are comfortable with them.
As an aside, I also like MyDefrag http://www.mydefrag.com/