Without a doubt the best Star Trek mod is: (drum roll please) Sacrifice of Angels 2.
The Borg will eventually destroy you if you let them tech/macro up.
This is an awesome mod and I love it when I am mired in a balanced game that lasts for days across multiple star systems. Don't forget to make multiple saves so that you can hop around and enjoy the modeling work while your fleets are devastated.
It's the waiting that is hardest. Knowing they're out there. Circling. Probing. Then darting in for the kill.
The Borg will haunt you in your nightmares.
You were warned... Fly You Fools!