I messed up a system real bad the first time I ran a 'registry-fixing' program, so I'm extremely careful now. I really wish that I had checked the details of the CoolWebSearch alert I got from Counterspy, but I was a bit jumpy I think, because I know that's a nasty one - so I deleted it, whereas I quarantined the other things. I'll check on those later, and see if they really were problems...
My system currently has 1400 (or so) 'errors'.
Of course these include all the links to MS's missing help file features, encrypted links to applications (again an MS favourite trick in MS Office), dummy links to allow hooks to external tools in quite a few apps.
OK there are a lot of 'orphan' entried, but apart from making my registry larger they don't actually DO anything bad to my system.
Personally I feel life is too short to work through 1400 cryptic errors and a range of potential soutions. So maybe I should use the automatic fix options (usually just delete all and sundry) .... not on your life.
By all means fix errors that cause specific problems (if you have the expertise, and not many of us do - certainly not me) but you are probably best leaving well alone and asking for advice when a problem needs to be solved. The Micrsoft news groups are excellent for this with some very knowledgeable people who give freely of their time and energy.
The only thing I do these days is periodically I compact and defrag my registry, mainly because I am always installing and uninstalling stuff so the registry can get a bit inflated and scattered all over the hard disc with consequent system crawling ....
There are lots of utilities that will do that for you, an alternative method is to get a decent defrag program (such as Raxco's Perfect Disc) and then after a full defrag (including system files) backup and restore your registry using the MS backup tool in Windows XP or 2000. Chances are you will end woth a defragged registry.