I use it mostly naked. That way, if I end up on a machine with an stock version, I can deal with it.

Have whatever mode you need for your programming language. Turn off evil crap like inserting tabs. Turn off the splash screen.

Swap your left capslock and ctrl keys (externally).

Learn the important key bindings and a few other tricks and you're good to go. That way you can focus on accomplishing something rather than spending oodles of time customizing your environment.