This is the sequel to Star Trek: 25th Anniversary and is in my opinion the best Star Trek game ever made. This CD-ROM Collector's Edition features voiceovers by William Shatner, Leonard Nimoy, and the rest of the gang.
Judgement Rites includes 8 new puzzle-solving missions and is almost identical to it's predecessor in terms of gameplay, but there are small UI changes that I found extremely helpful. Best of all you can opt to completely skip all of the arcade-style battles and get right to the missions.
As this is an older game you will need DOSbox to run it. (Be sure to read the included instructions.) After playing 25th Anniversary I didn't have any problems getting this one up and running on my machine.
The full manual is included in the form of multiple PCX images. You will need to print out the two starmap pages to get past the lame copy protection. (Again, exactly the same as 25th Anniversary.)