I'm finish a prototype which I want to make in a PCB board.
There are a lot of ProtoShield for Arduino UNO, few of MEGA and fewer for DUE.
For UNO it is also possible to download the Eagle PCB schematics.
How much they are compatible? since there is a voltage difference between the processor.
As far as I can tell the physical placement of the pins on a Due is identical to a Mega. So an empty protoshield will work on either. If you aren't using any of the pins on the 2-row header (and you don't need the space on the shield) then a normal Uno type shield will also work.
The protoshields aren't specific to voltage. There's no components loaded on the board when you get it so you can put anything you like onto it. You may find that some protoshield kits come with one or two LEDs and you would have to use a different resistor to get the LED up to normal brightness on a 3.3v Due. I generally don't use the LED holes on my protoshields, so those parts go straight into my parts bins.
I have one of these, it works fine on DUE and Mega2560, because there is both 3.3v and 5v available on the shield, you can decide what supply voltage suits your needs.