much hope to see UT3 and while using 2, i've got an idea- how about making a feature to check few(or more programs) in one turn, and then UT searchs for leftover files of them all? it could save much time when testing and then uninstalling bunch of soft
but maybe you already got such idea, or planned UT3 uninstall-behavior conflicts with such, than it's ok.
Update: Uninstall Tool 3.2 is able to perform batch force removal and batch remove entries!!