I agree with Wyatt's point.

Wouldn't there be an easy way to reset the last access date on all of the
files to say 1/1/2009 on a system then execute a relatively robust
multi-user boot (and maybe a world emerge upgrade) and record which files
are actually used during that process, then determine which package they
belong to and label those with some "level of criticality"?

Its probably also true that this list of files could be part of a "critical
system backup" that one could just keep around in a bz2 file for fast
recoveries (or even as md5sum's to determine when they might have been hosed
by disk errors or viruses) -- or is this something that is already done by
some of the selinux options?  [I've never used selinux so am unsure of
everything it does.]

R.