I've added initial Mega 2560 support to the logic analyzer. Please check it out here:
The Mega 2560 supports allows 8 channels (using PORTA, pins 22-29, but you can configure it) and 7K samples. I have done some basic timing tests and it is fairly accurate. I will tune it with my Open Bench Logic Sniffer soon, but it seems very usable already.
Please test it and let me know how it works for you. I've added the two device profiles to the repository so they're easy to find.