Alas, space sims are a dying (dead?) genre, and it's a big shame. The Freespace games have been fantastic, and the ending of Freespace 2 was not only hugely epic, but left a lot of potential for a third entry into the series, that sadly never came and likely never will. Freespace 3 is my #1 wishlist game.
Jumpgate: Evolution and Black Prophecy are both going to try and re-create the manual piloting feel of space sims. EVE is a fantastic and deep MMO (and can be free once you're able to earn enough ingame money to buy game time with, 100% legit), but it's not a combat sim as such. You tell your ship to shoot, and it shoots. Black Prophecy looks pretty decent, and is supposed to be a free-to-play MMO though as is always the case with those, there will have to be micro-transactions to support the model. Jumpgate has been fairly quiet for a while, I think they showed something off at E3 but I haven't seen anything since.
X3: Terran Conflict is a fine game, and a lot of the UI got needed overhaul from X3: Reunion. Eventually, though, I found myself wishing that the races were controlled by AI becase as it is, it's a dead universe - they have no goals, and they don't *do* anything. They're just there, governed by scripted automation, and nothing really happens without you.
I'm a heavy EVE player, myself, but keeping an eye out for Black Prophecy and Jumpgate.