GLX-Dock now has 2 new visibility modes: “hide whenever the dock overlaps the active window” and “hide whenever the dock overlaps any window”.
The dock will hide itself anytime it could get in your way, and will be visible otherwise.
You can choose between several smooth hiding animations: fade-out, semi-transparent, move-down, etc.
To make things better, icons that should draw your attention (like a message in the Pidgin applet or an alarm in the Clock applet) are visible (and animated) even when the dock is hidden.
Desklets (applets that are detached from the dock) can also be placed on your desktop without preventing you from clicking on what’s behind.