Although not as high profile as games like Freespace and X-Wing, I think there are others that are worth a mention. Some have already been brought up in the thread, but here are a couple more contributions:
The Star Wraith series [http://www.spacecombat.org/] - This is a long running(since 1989 if you include early 2D iterations) indie series of space combat/trading sims that boast many features(in the later implementations) not really found in other space games, including seamless space/atmosphere transitions. I highly recommend Evochron Mercenary and Arvoch Alliance, the latest two games. As a bonus, all of his games have playable demos available, so there really is no reason
not to try them.
The Battlecruiser series and more [http://www.3000ad.com/] - This one is more worth mentioning than playing, so take that for what it's worth. But I'd say it deserves a little recognition for the series' ambitiousness alone, even if it is the sort of ambitiousness that would drive one to try to fly with wings of wax. Here's a blurb on the official site about the first game, Battlecruiser 3000AD:
Command and control a military Battlecruiser complete with manual flight control of 4 fighters, 4 shuttlecrafts, 4 all terrain vehicles in space and over gorgeous planetary landscapes. Assign orders to over 150 ship personnel including officers, engineers, medics, marines and fighter pilots. Mine planets and moons. Attack space and planetary targets using fighters, all terrain vehicles or marines. Deploy or extract personnel and items from space or planets. Orchestrate invasions in any part of a huge game galaxy including strikes against space borne starstations. Order your ships and personnel using a variety of commands such as search and destroy, strike, escort, defend and many more. Use transporters to beam personnel to and from surface strike zones. Attack surface assets from space using devastating orbit to surface weaponry. Launch probes to remote regions to gather intel and stage your attacks. Trade hundreds of items with dozens of stations and bases.
Sounds good, right? Especially for 1996? Well. Another thing the site admits to is that the game was "virtually unplayable out of the box." It also admits that the game is really really hard, but doesn't mention that at least part of this is due to the novel sized manual you need to be intimately familiar with in order to accomplish anything in the game.
Another thing that makes this particular game worth mention is that the creator, Derek Smart, managed to spark a flame war [http://flamewarfollies.com/] that lasted 7 years on Usenet. Seriously, the saga of BC3000AD was bad enough that it made Gamespy's 25 Dumbest Moments of Gaming [http://archive.gamespy.com/articles/june03/dumbestmoments/readers/index2.shtml]. Mr. Smart has gone on to make several other games, none of which met with much success, and he is still making them(with plans for a future mmo, aparently). If he ever actually gets it right he will have made the holy grail of space gaming. Until then, he's at least amusing to read about.
Is it bad that the good game series got less words than the bad one?