As in Lion, in Mountain Lion I disabled the annoying zooming rectangle that appears with each window opening.
Just copy-paste this single line in Terminal.app:
defaults write NSGlobalDomain NSAutomaticWindowAnimationsEnabled -bool NO
Just Smooth scrolling is now mandated throughout Mountain Lion, as documented by John Siracusa amazing review. Fortunately Mr. Siracusa also found a solution:
defaults write -g NSScrollAnimationEnabled -bool NO
In Mail.app > Preferences, I set New messages sound to None.
In System Preferences > General, I set Appearance to Graphite to tone down Aqua's distracting colors. While there I bump up Recent Items to 50.