Star Trek: Judgment Rites was named #96 overall among the “150 Best Games of All Time” by Computer Gaming World Magazine (15th Anniversary Issue--November 1996).
This floppy disk version truly had a long install process, usually over 90 minutes. This is because the game had to decompress the data after copying from the floppies - a slow process on the 386s and 486s of the day.
The star map acted as a copy protection scheme. With out the manual, you couldn't navigate to the next mission.
In the floppy disk version of the game, the Enterprise's computer held a huge library of Star Trek Trivia. You can search if for virtually anything from the original series and get an entry. (including some amusing easter eggs, such as information on the Guardian of Forever being classified) Sadly, for the Talkie CD, this database was lost because of their decision to use Majel Barrett as the computer voice.
The episode Light and Darkness was written by SF writer Michael A. Stackpole. He has also written a series of books set in the Star Wars universe (about Rogue Squadron among others), and a series of books set in the FASA Battletech universe.