The Kazharii Imperium web site predates PBW by a good few years... it has moved servers numerous times, but I still think it counts...
http://kazharii.spaceempires.net/
There is the Universe Ladder Forum, Hypercomm Central, which may or may not still be in existence (certainly isn't active anymore)... it predates
www.malfador.com (note that only a while after the release of SE3 did Malfador have their own web site, before it was on
www.crl.com or something like that
). Definitely years older than PBW.
http://pub205.ezboard.com/bhypercommcentral
There was also the SE Center, but that was killed off by the creation of these forums for SE4...
The Solar Outpost has been around since SE3 times.
http://www.solar-outpost.com