Oh, how life is so much easier with one partition for just Windows, and another for apps and data.
This is one I just don't understand on Windows, though.
What good does having apps on a seperate drive do you? none. With having a registry, you can't restore the system partition without hosing the apps, so why bother trying to seperate them from the system? It's a useless convention.
I keep the data on a seperate partition many times, but I've been starting to get away from even that. Just put it all in a directory (like c:\data) and write yourself a logon script to back it up to another computer each time you log on. :-) Only takes a second to run an xcopy over the 100-base-T switch... Or, even better, gigabit. Then, burn the directory to a CD now and then for even more protection.
The theory works for Linux, too... Only use rsync instead of xcopy and just copy your whole home dir. ;-)