Here are a few of my favourites:
1. Panning - hold down the middle mouse button to pan the drawing/board. As Richard said, you can even do this while in the middle of another command, such as route, move etc.
2. Zoom wheel - I used to dislike the Eagle mouse zooming, until I realised how it works. Use the scroll wheel on the mouse to zoom in/out and (this is the trick) the zoom is centered about the mouse so you can quickly move from the left to right of a schematic or board by zooming out and back in again - it's cool.
3. Text entry of commands - as a true Mac GUI user I didn't understand why we had text entry - until I started using it. It is so quick and easy to do add/move/net/name/value in a quick sequence using text commands - I find I can work much faster this way than by moving the mouse to the buttons all the time. Of course you can assign commands to function keys to, but on a mac I like the default actions already on the function keys such as Exposé, Spaces and iTunes shuttle commands etc.
4. Spaces (Mac only) - set up 'Spaces' to have your board in one window and schematic in another and it's so easy to swish between them (yes thats swish not switch!) the schematic slides out and the board slides in - and you can even have data sheets and the farnell website in another to spaces. If you're on a mac and have never used Spaces or Expose I highyt recommend you give it a try. Simples.
Do you have any others?
-Kenny.