When working in Photoshop and Illustrator, I frequently have problems with the hidden dock popping up and interfering with something I am trying to do at the bottom of the screen.
But if you keep your document in Full Screen Mode (the one without the menubars), the dock will not pop up. Hit 'f' to cycle through the screen modes. Full Screen Mode is the one with the black background.
The only dowside of this is that the main menubar does not appear at the top so you have to be a pretty skilled power user to work in that mode for very long!
Mac OS X Hints
http://hints.macworld.com/article.php?story=20020914083258984