1. 25th Anniversary/Judgment Rites
While the three TNG games formed a loose trilogy, 25th Anniversary and Judgment Rites were always intended to be two parts of a story. Both were released on DOS systems, which make them impossible to play without software like DOSbox, and feature no tutorials, which them difficult for inexperienced players to get into them, especially when dealing with the starship combat segments that can't be avoided in 25th Anniversary. However, both manage to capture the feel of TOS through the point-and-click gameplay, especially when you play the versions with the full cast audio (which happen to be DeForest Kelley's last performances as Dr. McCoy before his death). While these games don't offer a great deal of playtime (there's slightly over a dozen levels between the two), they do provide an experience that can never be replicated today and form a major part of Trek gaming history that deserves to be seen by a new generation of Trek gamers.
What Trek games do you think deserve to be on the list? Feel free to drop them in the comments below.