Here's a question about the Foundry... if a user creates a mission that is identical to an episode from any series (recreated with same dialogue), would there be an copyright issues with that?
If it's identical down to the actual characters (with NPCs representing the original actors, etc.); yes, it would get flagged.
If it's a hybrid (ie same basic plot, but with original characters, altered dialog, etc.); no.
Basically the EULA and TOS states you have full use of any of the Star Trek IP settings, etc. From TOS through Nemesis; WITH THE EXCEPTION OF trying to create an NPC or likeness of any of the Trek actors. You can refer to their characters, and even use the characters 'off screen' per se; but create an actual NPC that you say IS 'Captain Kirk' (and attempts to capture William Shatner's 'look') is pohibited; because SAG actors retain all rights to their likeness in any media; and said likeness CAN'T be used without permission or compensation.