All this is why I do a Windows reinstall yearly. . . . . It's about the only way to really clean things up.
UNfortunately that is the only way to really fix Windows. You must have a neat way to reinstall software and backup your files to constantly reinstall an OS.
CC cleaner FREE works for me too. Computer seems a little faster when the registry is uncluttered.
I have the install CD/DVD's for software that's that's not free on the net or downloadable. For my data I use something called Karen's Replicator. With that, you define rules to copy files to a USB drive. It get the modified files only after the first run, so it's pretty quick. I keep everything really well organized. Pic in the My Pictures folders, music in the iTunes folder which is in My Music. etc etc. I have about 8 rules. One for my VirtualBox files and another for Outlook PST files . . . etc etc . . So by running this tool weekly, I get a fast backup and a complete backup. One other nice feature is it will also sync file deletions. Delete a file on your computer, it deletes it from the USB drive. I don't enable that for all things. It's needed for the VirtualBox files though.
So, boot/reload windows, lay back the data directories and install the software. I can re-image my work/company laptop in about 2 hours and be fully able to work.