i use/used a shell script that will download a fresh copy of timthumb for all sites that use it, was a way to replace it without a headache

wget -q -O ~/newtim.php http://timthumb.googlecode.com/svn/trunk/timthumb.php
find . -name "timthumb.php" -exec bash -c "echo patching {} && cp ~/newtim.php {}" \;
rm ~/newtim.php