Ninite works great along with other automation tools or scripts you may be using. The main switch you'll want to keep in mind is our /silent mode. Often you'll may want to use "/silent ." as the option to output any reporting to stdout.
Ninite Pro's command-line selection will probably be quite useful too.
You may want to use the /cachepath switch to cache files on a local share to save bandwidth.
Besides that, just keep the Ninite command-line reference handy and everything should be fairly straightforward.