Things I need to remember when updating to Mountain Lion. This list could well grow over time ;)
Paths - /etc/paths get's written back to standard with /usr/local/bin last
Permissions on /usr/local
Machomebrew needs /usr/local to be writable - remember to reset ownership after update.
Command line tools - XCode
Reinstall command line tools from xcode before running any machomebrew updates.
Run Intellij (or other java app) to trigger an install of a JVM.