Bottoming out keys = you press the key until you can't push it further.  The key actually actuates when you push it down half way (after the click you hear and feel).  I believe the idea is that you can get faster typing speeds by not actually bottoming out the keys.

To be honest I can't tell if a mechanical keyboard is really that much better.  The clicking noises are cool and all, but IDK if I'm actually typing any faster on it...