Starting with today's Moksha update in the unstable branch Moksha now supports a "startupcommands" file in your local directory.
Specifically the file ~/.e/e/applications/startup/startupcommands is executed on the startup of the desktop. Simply place commands you wish to be run in this file separated by a pipe and they will be run as expected.
For example if I wanted to launch VLC and ePad at startup the contents of my startupcommands file would be:
vlc | \ epad
I am hoping to get the Swami startup applications module done later this week that will serve as a GUI for adding startup commands / applications easily.