I get an error if I change the prefix in extras/contrib/config.mak to /usr
I get something like this (don't remeber exactly what was wrong)
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cp -R /usr/share/aclocal/* ../../m4/ ERROR no such file or directory
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cp -R $(PREFIX)/share/aclocal/* /Users/simon/Desktop/vlc-svn/vlc-trunk/m4/
btw. I have a G5 optimized build of VLC