I use Ace Utilities. It offers everything you need to clean your registry, junk files, program-startup list and history - and it's also the SAFEST utility I've found for registry maintenance. In default mode, it uses an exclusion-list of registry items that, if removed, might harm system operation. 30-day free demo is fully-functional, $30 to buy.
The only feature it lacks is a manual registry-search function, which they feel would make it 'unsafe' for the typical user. I use JV16 PowerTools for manual search of the registry.
Hope this helps!