StarTrek.com
The official site

Paramount
Licensor of Star Trek. They have Trek DVD's here

Taldren
Developer's of Starfleet Command III

Battleclinic.com

Dynaverse.net

Star Trek Gamers.com

Trek-Online.com

Clans playing on Alternate B

Galactic Foreign Legion

Klingon Honor Brigade

Rihannsu Tal Shiar clan

Scorpion Pirates clan

StarFleet Command

Valkyrie Fleet Command

Let me know your clans web addy and I'll add it here

Other Servers

Alternate Universe

Chaotic Network

Maquis Destructive Force

Near Distant Future

Rebel Alliance

The Q Continuum

SFC3.Puterz.net

One last piece of information

Activision
Publisher's of Starfleet Command III.
However, they have removed all Star Trek games
from their system...at least I can't find any.
(It has a lot to do with the lawsuit)
That's why they are at the bottom of the list.

Know of a link that should be added? E-mail me!