Uh, is MOO3 even out yet? That's one
I don't know much about it, but here's a few good points about SE4 (Gold)
-extensive mods already available, more possible
-graphics for many favorite SF races
-good custom race creation system
-good pre-game setup options
-simultanious or sequential play
-Play By Web (like PBEM, but the site does all the work for you)
-TCP/IP support
-really good developer support, a lot of the stuff in patches comes straight from requests. Sometimes he manages to give us stuff we hadn't known we wanted yet
-good ship customization system
Phoenix-D