Ninite Pro can generate a report showing the install state of all the apps Ninite knows about, their current versions, and if they can be upgraded. The command looks like:
NinitePro.exe /audit /silent audit.txt
And an example snippet from the audit report looks like:
iTunes : Not installed
Java : Update - 6.0.220.4 -> 6.0.230.5
JDK : OK - 6.0.220.4
That means iTunes is not installed, Java can be updated to version 6.0.230.5 (the current version is 6.0.220.4), and the JDK is installed and up-to-date at version 6.0.220.4.
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.