Ninite Pro supports command-line app selection. This lets you use Ninite very much like a version of Debian or Ubuntu's apt-get for Windows.
For example, here's a command to silently install Firefox, Skype, and both the NPAPI and ActiveX versions of Flash Player:
NinitePro.exe /select Firefox Skype Flash "Flash (IE)" /silent report.txt
The installation status is written to report.txt for later review.
You can name one or more apps to install after the /select switch. Here's the list of supported applications and their /select names. You can also get a list of available apps and their latest versions by running:
NinitePro.exe /list /silent apps.txt
You can use the /exclude switch to exclude applications when using /updateonly or /audit mode. The following command updates all applications that are out of date, except for Java and Python:
NinitePro.exe /updateonly /exclude Java Python /silent report.txt
Please note that the /exclude switch is only useful in combination with /updateonly or /audit. If you're already using /select to pick specific apps you would exclude an app by simply not listing it after your /select switch.
These features are only available in Ninite Pro Classic.
We're working on documentation for the new Pro web interface. For now the available help for that is inline in the interface.