I've now got a full set of Atmel Xplained Mini Eval boards: atmega168pb, atmega328p (practically an Arduino clone), atmega328pb, and SAMD10.
They sell for less than $10 each (and are sometimes swag at trade shows or seminars), and include an mEDBG chip, with provides debugging (with Atmel Studio) as well as USB/Serial functionality.
The 328pb is the most interesting of the lot - in a blaze of poor naming, Atmel has added a bunch of features to the 328p (more timers, 2nd uart, 2nd TWI, touch controller, (documented) unique chip ID, AND MORE!)
And yes, you can stick a bootloader on the AVR boards and use them with Arduino. The boards all "feature" the Arduino "shield" pinout.
The mEDBG chip is a little young (doesn't work quite right at 115200bps, for example.) It implements CMSIS/DAP; an ARM-standardized debug access protocol, which they use to "wrap" AVR debug commands as well. It's not clear whether this will ever allow non-Atmel debugging; I don't think they're documenting the AVR debug commands, so the fact that they've documented "use this CMSIS/DAP command to wrap an AVR debug command" isn't very useful (why, Atmel, why?)