Palliser:
USB host behavior? What functionality does that give you? Is that where it can act as a keyboard or mouse, or is it where it functions as removable storage media? Or does it allow it to interface with mice and removable storage media directly?
Graynomad:
My current board uses the 1284P. It's nice, with an extra timer, and USART, so I have three SPI channels and enough timers to both play sound from an SD card and update servos, and it sure has a lot of ram, but it's still only 16mhz, can't be programmed via USB without an additional chip, requires an external resonator to get to 16mhz, has no built in DAC so I have to add a chip for that, and costs more than the SAM3S.
If I were to go that route, and go with a minor upgrade to 32mhz and two 12bit DACs, I'd go with the XMEGA128A3U or 4U. Problem is, I don't really gain much by doing this. I no longer need a DAC, but now all my data lines are 3.3v which complicates my design. (I was connecting everything with servo cables but can't do that if I have only 3.3v to supply, and can't supply 5v on those pins with the IO needing a 3.3v input... hm... well actually the switches do pull to ground, so I guess I could still supply 5v to those pins for the servos. But I don't think servos like 3.3v logic.) So there's no significant benefit to such a minor upgrade for me.