Autonomous Robotic Hardware Development
I recently got one of these...yeah!! I will be using this with YAGARTO and MDK-ARM (free 32KB limited edition).
The Atmel SAM-ICE debugger is available for all Atmel ARM targets which includes a free GDB Server license.
There is a good tutorial regarding its' use with the YAGARTO tool chain, http://www.yagarto.de/howto/jlink/index.html
This provides a good way to play around with the ATSAM3U internals and get to know its peripherals.
Others may opt for the J-LINK EDU edition, relatively inexpensive and designed for any ARM7 or ARM9 target as long as it is not used for commerical product development.