I've often gotten frustrated with my /etc/portage/package.* files when they become massive and full of crud that I don't even have installed any longer. Because of this I have crafted a simple little utility to clean out packages that are no longer installed and USE flags that are no longer valid from these files. This should help trim the cruft from the Gentoo configuration.
pclean, does all of this and only has one major problem (so far) before I call it good enough for a 1.0 release. If you would like to try this little utility; it's available in my overlay and if you notice any odd behavior please report it to my bugzilla.