Let me add a few games to JT's excellent list.
First, similar to the Wing Commander series is a game I haven't seen mentioned: Starfleet Academy.
Much like Wing Commander there are interactive movie segments between simulator missions, but also within the missions themselves as you try to solve things with diplomacy instead of shooting. There are a few different endings depending on how you choose to manage the other cadets under your command and how well you do in your missions since there are often multiple ways to go about succeeding. It has appearances by a few original series actors, especially William Shatner and Walter Koenig.
https://www.gog.com/game/star_trek_starfleet_academyAlso on the topic of Wing Commander, Chris Roberts did another game series with FMV and this will probably be the one I'll be playing for April since I never got into it before. They're isometric action games with frequent FMV sequences.
Crusader: No Remorse
https://www.gog.com/game/crusader_no_remorseCrusader: No Regret
https://www.gog.com/game/crusader_no_regretOn the Myst side of things, don't forget the time travelling adventures of the Journeyman Project series.
https://www.gog.com/game/journeyman_pro ... _prime_thehttps://www.gog.com/game/journeyman_project_2https://www.gog.com/game/journeyman_project_3Another great game that was passed up back in the day in favor of stuff like Quake is an early example of a tactical FPS with its own corny FMV story. Terra Nova: Strike Force Centauri.
https://www.gog.com/game/terra_nova_str ... e_centauri