Got a Due today, started playing with it, and put a custom shield on it that was designed to be powered by either 3v3 or 5V from the ICSP header. Assumed the Vcc on the ICSP header would be 3v3, so that's what I set the voltage selection jumper to on the shield.
Just before I plugged it all in, I had a thought that I should really check what voltage (if any) I was getting from the ICSP header (well, really SPI header since it doesn't do ICSP, but you know what I mean.)
So got the multimeter, and guess what? 5V. Surprised, but saved me letting out a bit of the ol' blue smoke.
AFAIK, ICSP doesn't specify 5V, so not sure why this pin would be connected the 5V rail rather than the 3v3 rail. Only reason I could think of was to make it more idiot-proof in case someone decided to try programming the Due with a ICSP programmer, and might blow it up by putting 5V on the 3v3 rail via the programmer.
I don't know -- maybe there's a better reason. But in any case be warned -- look before you leap on a hybrid 5V/3v3 board!