I haven't done it with a Mega2560 chip, but for the past year, I've been running the 328
chip at 16Mhz and 3.3V, and the past month been doing same with the 1284P chip. And
no problems, although against all warnings - of course. If you interpolate the operation
curves, they actually show 13.3 Mhz at 3.3V, so you're only overclocking by 20%.
Also, for hacking, the 40-pin DIP 1284P chip is a nice choice inbetween the 328 and 2560,
and lots easier than tiny smt pins. You get 32 I/O pins.
I actually ordered one the other day. It is in the mail.
I am actually not all that impressed with the pin mapping on the ATmega2560. I like to do a lot of tricks reading an entire port with a mask or writing an entire port at once and the way they pin-mapped this, it is all over the place to make it work with existing shields.
Good to know about your experience with the 1284 as I was planning to do just that with it.