I use Erunt which backs up the registry daily automatically and behind the scenes...it also has a tool that optimises and compacts the registry...
As to a cleaner for years and years i have used Total Uninstall. It is run before any programs are installed, records all changes made and takes a snapshot of before and after.
When i uninstall something afterwords i just run TUN and revert back to the way things were...no wayward .dll's, no bloated reg entries.