http://www.mathworks.com/access/helpdesk/help/techdoc/ref/matlabunix.html#matlab_unix_refpage
matlab -nodesktop -r mystuff.m
or
matlab < mystuff.m > myoutput.txt
the -nodesktop tells you that < piping does same as nodesktop.
I also noticed that the various blocksets (eg communications) have help stuff like: use sim("mysimulation") to run the simulation in the background and also how to set up multiple simulations of the same thing.
-- DanGrimm - 23 Nov 2007