I arrived at the PC market just a tad late to have played Dune II, but it was the first RTS I ever heard of by way of schoolyard chatter. It's possible that hearing friends talk about the game was my first exposure to Dune and its principal elements—the Atreides, the Harkonnens, the spice—before I knew any of that came from a major science fiction novel or a film.
Anyway, here's something I'm quite confident nobody will name (and which I had trouble hunting down from my faint memory of it myself):
This is
Trek, an unlicensed Star Trek game on Apple Macintosh System 6, and the standout title from the Mac shareware/freeware floppies I used to comb through in the early 1990s via the public library. A grid-based starship simulator, I honestly remember it to be the best Trek game I've played, though I haven't touched it in over twenty years and would need to assess it again with fresh eyes to know how well it holds up.
There are a ton of Mac obscurities from that era that outclassed their contemporaries on MS-DOS in control and interface design (but fell behind in support for colour), products of a healthy shareware community (an ancestor of sorts to today's indie market) that was necessarily restricted by the platform it was on, especially with Apple entering a period of serious trouble which established the reputation that Macs still have today as computers not known for serious games. I'm still trying to retrace my way to a space 4X from that era as well as some HyperCard puzzle adventures.