I use the PC Tools Registry Tool which, although its paid for (not a huge price), works very well. The Windows defrag and cleanup tool is known to not be the greatest although its certainly better than nothing.There are several MUCH better Registry and other Defrag tools out there!
The Registry eventuallygets very bloated and loads of detritus gets left behind with installs and downloads etc which can lead to problems and slow performance, even system crashes. I'm a great supporter of "free" software, and a lot of stuff out there is pretty good, especially if you run Linux, but I also believe you generally can expect what you pay for and all software, whether big name or one man band proggies, takes someone time and resources to develop which is not "free."
There are a lot of rogue programs out there though, seeking to scare people into shelling out unnecessary money on "fixes" , some of these are even trojans or malware of a kind, so best to check before using / buying into any of them.