ComputerCraft scripts - I run a wireless network in-game, and I have them all re-download their respective script when they start up. This way, I can change the program once and all the computers that use it will receive the update automatically.

Skynet (my wireless network, and yes it's supposed to be funny)

Store them on the computer as "startup" to run these scripts when the computer starts. Good for relay scripts, so you can have hundreds of relays auto-start on world load rather than having to manual start them all.

Relay tower script: http://wordenhome.neocities.org/download/cc/sk/relay.txt