Depending on the number of packages installed, and the computing power of the build system, I've found that
taking a list of the current user-installed packages,
moving ${PREFIX} out of the way,
re-bootstrapping (just takes some cycles on NetBSD, needed on other platforms),
and rebuilding each of the packages on the list that was taken
should DTRT, even in the face of major package version bumps (assuming python/perl/postgres/mysql and friends are installed as prereq for something more usery-level). If there's fallout, nuke the new ${PREFIX} and move the last good ${PREFIX} back in its place. I have a simple script to achieve this, should anyone want it, but it's kinda hardcoded to me; it could be made more generic, though
I think tnn posted that he used something similar too just recently.