I may have misread your request. For some reason I thought I read you were looking for a program that will tell you what categories your downloads fall into. Clean installer will do that (tell you if something is a clothing item, accessory, etc.) It will also highlight hacks and mods in red, to help you find them all. (I keep my mods in a separate subfile so I can easily pull them out)
One small caveat about the HCDU. It won't tell you what the conflict is, it simply identifies the mods that alter the same global procedure, thus letting you know what mods
may hack. Just because they're there, doesn't mean they are conflicting or will, but it's a good starting point.
As Alisdair said, the more information about what exact problem you're having, the better we can help you.