Freespace 2 is probably a nearly unanimous agreement. Though this isn't a space combat sim per se, Evochron Mercenary is a current favorite of mine; it's quite sand boxy.
My personal favorite. REAL FUCKING PHYSICS! I love when one of my friends starts blasting forward at near 300 km/s an hour and surpised when they can't go reverse almost instantly. Well dude you are already traveling near light speed forward, you didn't expect you needed some time to slow down?
Also pulling some sweet manuvers in the engine is very satisifying, like going forwad, spinning around 180 degree's while still maintaining current trajectory so you can blast the asshole on your tail.
Since I haven't played Reunion or Albion Prelude, I'd say X3: Terran Conflict. Amazing visuals, detailed ships, a crap load of ships to choose from, pretty good dog fighting, can create massive trade empires, or tear shit up with a massive fleet, or both. But damn all that micro-management! This is one of those games that you pretty much have to play with mods. The stock game is just too slow and too peaceful for me.