Chiliflash. Basically it's a serial app that sends a ZCX and reads back status. I've never been able to talk to these things with a serial program like PUTTY, never know the baud rate or stop bits. Oh well, someday.
I haven't tried to download the code yet, if the ROMs are protected that won't work. I don't think the Atmel will brick if you just try to read, I'll give it a shot tomorrow after running for a day with no problems.
Haven't tried chiliflash, but yesterday I tried my AVR Dragon and Atmel Studio for the first time ever. I bought a Jalapeno again just for testing it and flashed in a 1.29 firmware to try it out.
And today I gathered all my courage and tried it on my 550 GH Monarch. I was surprised to find the same Atmel controller on the Monarch that the Jallies had. And when I powered up the Dragon the Monarch somehow reset itself and overclocked itself from 650 to 710 GH. It was a bit terrifying experience when cgminer started spewing errors when I browsed through the device programming pages on the Atmel Studio. But yeah, the Molly didn't brick itself as a revenge for trying to read the secured firmware.
So what's next? We're waiting for somebody to post the firmware source code to wikileaks?