A better Terminal iTerm2.
Media Player VLC.
Dropbox.

Developer Apps

GitX, rowanj fork.
FTP Client Cyberduck, use to be a favourite on Leopard & Snow Leopard but it requires a java runtime which does not come by default with Mountain Lion. A Cyberduck will prompt to install a Java Runtime but I would prefer not to install unnecessary things. Transmit or Forklift both NOT free look like good alternatives.

Unix Applications

brew update
brew install macvim
brew install tree
brew install wget