in the window menu, you have workspaces. In there are the factory default settings and you can also save your own default settings. If you have a dual monitor setup, be aware that there are a few panels that (pretty much) won't remember to stay on the second screen.
Is there any way to PREVENT the palettes from docking?
This docking business seems to have crept in with CS3 and I find it rather infuriating. Palettes often seem to go there by accident.
I much prefer Photoshop's docking - is there any way to position the dock at the top?