The only program I have used for destroying things utterly (though manual) is called FileAssassin. It deletes anything no questions asked beyond "are you sure?" and does not care about access permissions either.
Note: this is very powerful in the sense it will ignore warnings about sensitive Windows files so you have to be certain you are not deleting something integral to your system.
Depending on what you're removing it may be a good idea to search for uninstallers made specifically for removing said program. As an example I had issues with iTunes not removing from my system entirely and used a utility called ByeTunes which existed for the sole purpose of removing iTunes program traces.