I'll second GNU Stow — I've been using it off-and-on for almost twenty years now (hard to believe that it's been that long!). It does have issues when pre/post-install scripts are required, but that could be easily wrapped.

I think Stow could be easily combined with the ideas in this article to yield something pretty awesome. It already supports clean uninstalls and checking for conflicts, and individual Stow dirs are easily tar-able too. Really, a wrapper around Stow that knows how to handle common configure/make/make install patterns sounds like it'd do the trick.