I need to power the DUE with its 5V Pin in normal operation. What are the side effects of this?
Is there any component used in an unspecified range?
I guess one should also avoid connecting the DUE to USB while having the 5V supplied at the 5V pin.
Is there a suggested modification to the board?

I would like to use an external 3.0V reference for A/D conversions.
Looking into the schematics, the related pin on the SAM3X8EA is connected to a (filtered) 3.3V supply. The AREF pin in the standard version of the board (mine is R3) is therefore simply a 3.3V output.
On the other hand, the board seems to have a provision to make a simple change to allow to use the AREF as an input to the SAM3X8EA. There is a small white rectangle drawn on the upper side of the board, with the text "3.3/Ext" above and "AREF" on the right of it, nearby to the ICSP connector.
Can anybody tell me what change has to be made?

Thanks Nick to have solved the problem for the Mega2560 (now only the correctly working bootloader should be delivered with new Mega 2560 and new versions of the IDE).

Meanwhile, I have ordered the new Arduino Due. Has anyone yet successfully used watchdog with this one? Means, does the standard Due bootloader support watchdog, and what are the equivalent lines of code for the SAM3XE8 in the Arduino IDE?

Regarding "
Tested on the Mega2560 board once I replaced the bootloader with this working one:

https://raw.github.com/arduino/Arduino-stk500v2-bootloader/master/goodHexFiles/stk500boot_v2_mega2560.hex
"

I found another bootloader (which seems to be the one installed with the Arduino IDE) under
https://github.com/arduino/Arduino/tree/master/hardware/arduino/
bootloaders/stk500v2/stk500boot_v2_mega2560.hex   

It has the same file name as "this working one", but its size is 103kB versus 21kB for the other.
Obviously, these are different bootloaders, and should have a different version, means e.g. stk500boot_v3_mega2560.hex for the working one. Besides of this, what are the differences between the two, other than watchdog support?

Thank you for the hints...with complicated, I just meant, I spent hours in the internet to find out in principle what to do. I know Arduino aims more on beginners than on hackers, but nevertheless, Arduino is usable for serious applications. And watchdog is missing in the libraries.
Main thing is, I agree, to install the proper bootloader. Why does the pre-installed bootloader not deactivate the watchdog? This should not really be a technical problem, is it?
Anyway, do you have a link to a bootloader that officially supports Arduino Sketches on a Mega 2560? Sorry if this is a silly question, but I have no special knowledge which bootloaders are available and which one to use for which application.

Thanks for the hints - I knew that there is only one ADC, but did not have this in mind when I wrote my topic. Nevertheless, my suggestion makes sense, it just means one could start a conversion for a certain pin, doing some other processing, read the result, starting conversion of the next pin, and so on. The point is, not to waste processing time while waiting for the sample and hold capacitor to charge and performing the conversion.
@Groove: I would be very happy if I could implement this in 10 Minutes.

The current Arduino Library (coming with IDE 1.0.1) only has one function to read analoge inputs. Since the conversion is started with the call of AnalogRead and the function waits until the conversion is complete, it is one of the most time-consuming function calls. Reading all 12 inputs one after each other lasts therefore ca. 1ms which is a long time if the sketch needs high sample rates or performs other time critical functions that have to wait for the conversion.
It is possible by register manipulation to increase the clock speed of the A/D conversion, but at the cost of 1bit accuracy with respect to standard frequency - and the register manipulation is processor dependent.
I suggest to have an additional function that allows to start a conversion but comes back immediately (e.g. naming it "AnalogStart"). The AnalogRead should then check whether an AnalogStart has already been called (means conversion is already in progress) and wait for the result; otherwise internally call AnalogRead first if one does not care so much about speed and staying compatible with existing Sketches.
This would allow to start the conversion of numerous analog inputs before the result of the conversion is needed, and then later to quickly read all of the analog inputs.
Especially for the new Arduino Due, it would be very unsatisfying to have a 32Bit ARM CPU with 87 MHz but still have to wait such long times for analog conversions.

I think watchdog support is essential for many projects where an Arduino boards performs control functions 24h a day.
Reading many posts in the internet, it seems to be very complicated using Arduino 1.0.1 and the current standard bootloader for the AVR boards to get watchdog functionality working. One issue is, that there is no watchdog function in the Arduino Library that would allow processor-independent implementation of such function; currently, registers have to be set directly. The more severe issue is, that the bootloader does not de-activate the watchdog upon reset, so that one can end up with endless resets. There are patched bootloaders available, but without official Arduino support this remains tricky.
Please, at least starting with the new ARM processor generation of boards, support watchdog with a compatible bootloader. If feasible, dedicated library functions should be added to initialize and reset the watchdog.