Regarding /etc, here's my method that I've recently started.
After *completing* an upgrade, I touch a file (say /.lastinstall);
thus I know any files newer than that have been done as customizations.
After performing a new upgrade, I run 

    find /etc.old -newer /.lastinstall -print > /tmp/newfiles
    touch /.lastinstall

and then hand-copy the relevant files over.  Note the *copy* to cause
the copied files to have new time-stamps, so they can be identified
for the next upgrade.  Worked well for my upgrade from 1.5_ALPHA2 to 1.5.

-- 
"Maybe this world is another planet's Hell." - Aldous Huxley