The thing that confuses me the most about it is when I close the last window of an app, 95% of the screen shows the app beneath it but the menus are still for the app I just closed. I guess that's partly a crossover with the focus model as well, but it's just a bit alien to me. As you say, it's really a non-Mac user thing; I only use OSX 5% of the time at work so never really get used to it.

I really don't see much difference in clutter between minimising to the taskbar and having an icon on the dock.

It's odd to hit the x to close and the program actually just minimizing. Odder still was that when I hit minimize, by default, it minimized to a separate icon to the main application. I changed to it minimizing into the dock icon. But the inconsistent behavior of the x button means sometimes it and the _ button (I can't call these close and minimize on this system because that's not what they are anymore) have similar, if not identical, functionality.

Huh? I don't think you understand what I'm talking about...

To prevent Firefox from closing, go to about:config and set browser.tabs.closeWindowWithLastTab to false. This is one of the first things I do when I (re)install a computer, I don't like the default behaviour either :)