The ones I remember off the back of my mind are Transcend and the JAD Trilogy. I also finished ST:R, which in my opinion is done with ingenuity, though I would recommend playing the original Silient Threat first (if you can), as flawed and broken as it is, if only to see the rather large differences done between the two.
Transcend is the first thing, out of the several dozen horror movies and games I've ever seen, to actually scare me. The writing and atmosphere is sublime. I insist you play that one. Sync, the prequel (I think?) is much the same, though I think Transcend is definitely scarier.
JAD, whether you get some of the in-jokes relating to Freespace 2 or the HLP community or not, is simply hilarious. That's also another one I insist you play. It has the most hilarious jokes I've seen in a very long time.
Inferno is worth playing simply because of the spectacle of it being a spiritual incarnation of a Freespace 3. I never liked it, personally, probably due to the fact that most of the sound affects were ripped right off of Descent 3. (
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I'm kidding. Inferno is really good, though most would agree the story is rather linear at best.
