Certain memory areas correspond to the console. If you have a look at Notch's Hello World example you see him putting letters in memory areas.

Now if this is how it will communicate with the rest of the ship, I don't know.

A few days ago he was thinking of a message queue... not sure how it would work though.

http://twitter.com/#!/notch/status/187448370107912192

Since he wants to simulate the cpus all the time and there's no sleep / wait which actually stops execution, tight wait loops shouldn't be an issue. Just wait for some mmaped [msg_no_ptr] to be >0.