Well, app exposé (I have it mapped to 4-finger swipe down) will show you minimized windows, so in your scenario I could cmd-tab over to safari and 4-finger swipe down to select the minimized browser window. Selecting from the dock may be easier in this case. I generally use a combination of 4-5 desktops with certain applications set to specific desktops, a couple like the Finder and iChat/Messages set to all desktops, cmd-tab for switching between applications/desktops, and cmd-~ for switching between open windows within an application--I don't generally minimize windows though.