On the cheapstat there aren't reallly any spare digital IOs which are conveniently available on a header or any thing like that. There are spare digital IOs on the ATXMega, e.g. PB0, PB1, PC0, PC1, etc., but the trick would be accessing them. You would have to solder a to the microcontroller pin/pad. Another option might be to the IO lines used for the SPI signals to IC4. This is a flash memory which isn't used by the current firmware. You could remove this chip and you would have four IO lines available at IC4 - CS (PD4), SI (PD5), SO (PD6) and SCK (PD7). Again you would have to solder to the pads - a pain, but at IC4 they are a bit bigger at least.
Another option might be the Rodeostat which has 2 expansions headers P13 and P14. Between them you have 16 digital IO lines you could use plus SPI and i2c bues. Both P13 and P14 use 5x2 shrouded headers which you can connect to with a standard IDC connector.