Can't believe no one has mentioned Battleship Forever, which was a major inspiration for Starfarer itself, and its predecessor Warning Forever, an Asian top-down shooter with lots, or rather, only boss fights against procedually generated battleships in space.
And, Flatspace I & II. Sort of Elite-esque with 2D gameplay in 3D graphic with view point similar with Sf.
Also...control-wise, NavyField can be configured like that with some in-game customization including fire control with mouse pointer, but that's a big-title MMO.
And lastly, you can't mention Transcendence without mentioning EV Nova, and there's also the turn-based Space Ranger I & II with simultaneous movement, mixed-in text adventures and delicious language localization, and another 2D turn-based spaceship fighting sim with similar movement style and no leading for its missiles whatsoever...Oh well.
All of the games mentioned, except that MMO and possibly Space Ranger, are indie.