I just noticed that Seedstudio lists as a feature for their Mega that ports F and K can be configured to operate at either 3V3 or 5V (I assume for digital IO). A single mcu directly supporting both 3V3 and 5V peripherals could be a useful feature.
Can anyone share some insight as to whether this actually works and also if the same would apply to an AtMega328P (for port C)?
Can't find anywhere in ATmega1280 datasheet something saying that the mega can be powered with 2 different Vcc. And if powered with 5V the inputs are not strictly compatible with a 3.3V output from another chip.
On seeedstudio they have put a warning telling "3.3V selectable for Port F and Port K (unstable performance on some boards, not recommended for current version.)"
I noticed the warning, but haven't seen any explanation. E.g. is the issue related to manufacturing, design or concept?
Looking briefly at the Seeduino Mega schematic it seems as if they use VCC and AVCC for the two supply voltage levels. VCC and AVCC appear to be separate in a number of AVR chips and it had me wonder if this could be used to support two different logic levels.
The 5.0/3.3 switch option design on the Seeeduino Mega is a design error, and the switch should be left in the 5v position only. Here is a posting on the matter from the Seeeduino support forum:
http://forum.seeedstudio.com/viewtopic.php?f=4&t=385&sid=8fc358051a7f39b07a26170cae318803
The next version of the board is said to redesign the power scheme such as the whole board will be either running a 5v or 3,3v depending on the switch position. OF course without changing the 16mhz crystal the chip will be working outside it's recommended specs if running at 3.3v/16mhz.
Lefty
It seems clear from the link posted by retrolefty that the whole idea of using different logic level supplies for VCC and AVCC is flawed. It does not work with the Seedstudio Mega board and an upcoming revision will abandon the idea altogether - so back to external level shifting. 
Thanks for the clarification.