Is there a list of commands somewhere?
Sometimes the people mean just basic Unix commands in which case I point them at one of our intro to Unix books. Other times the person really wants to know what all software we have available, what they can do on the Internet, etc. etc. etc. (I get this question during tours too which is why I made the TCC software page.)
Information on the software packages available can be found at Software Packages.
Information about Unix/Linux commands can be found at Unix / Linux commands.