If you check the Mightyboard RevE files on Thingiverse (http://www.thingiverse.com/thing:16058/#files) you will find the schematics and PCB files (.sch and .brd) for the version of the board used in Replicator 1s and (with some minor mods) most clones. The Atmega 1280 IO header section is a bunch of breakout pins for debug functions. There are eight sets of signal/5v/gnd groupings. Four of them are currently driving debug LEDs that show flash codes for particular firmware failure modes. The other four are unused as far as I'm aware.
The ninth and tenth pins shown in the schematic are located on the opposite end of the board, near the 8U2 chip, to give some hacking access to that chip as well. (The 8U2 handles USB comms and firmware flashing the Atmega 1280.)
If desired, you can build your own firmware using these pins for other purposes, such as signaling to external equipment. But building Sailfish is a little more difficult than just running the latest Arduino IDE (for compiler stability reasons) so the vast majority of Mightyboard users never bother modifying their firmware.