The question of whether UQM is violating copyrights or not is up to the law itself. And if they are violating copyrights, it is Stardock's obligation to act on it or else they weaken their position in regards to claiming those copyrights.
So, as mentioned in reply #15, there hasn't been any suggestion so far that Stardock has any copyright on Star Control 2, or on the UQM project that came from it. All of Stardock's claims that might give it any control over UQM are based on trademark.
Stardock does make a claim that some of the contractors who worked on SC2 might have copyright claims on it, but none of them have stepped forward to make any. And Stardock does claim to own the copyright to SC3, but SC3 is mostly irrelevant to UQM.
Also, to the best of my non-lawyer knowledge, only trademarks impose an"obligation to act"; copyrights do not.
I don't know exactly what the agreement was between UQM and Accolade or UQM and T4B...
There was no agreement between UQM and Accolade because by 2001, when the project was founded, the understanding was that Accolade's license to the Star Control 2 copyright had expired, such that Paul and Fred had regained all of the copyright rights, and that the only other IP limitation on the game was the "Star Control" trademark, which the project dealt with by removing every instance of the words "Star Control".
And the agreement between UQM and Paul&Fred (or T4B, if they'd formed it by then) consisted only of the two licenses (GPL 2.0 and Creative Commons BY-NA-SA) that they released the code and content under.
...but I've seen many other fan projects based on copyrighted material that had no desire to "engage in commerce" and wanted to release everything for free and were still sued into oblivion.
Certainly. If Stardock had the copyright on SC2, it would be an entirely different situation, because copyright gives control over copying even when that copying isn't "use in commerce". The "use in commerce" question only matters for trademarks.