Best Trek games? Well in my opinion, BC takes the cake. However, Armada II, and Birth of the Federation are on my top lists. BC provides the freedom, the video possibilities, mod capabilities. With BC, the possibilities are endless. Armada II provides me amusement. I love to spam Defiants, BoPs, or Warbirds. Nothing more frightening than a HUGE mass of small ships or LARGE, FAT Warbirds coming towards you. Birth of the Federation tests decision, management skills, and endurance. Allowing you to expand your empire in many ways, shapes, or forms.
Though Starfleet Academy, Elite Force II, and, believe this or not, Star Trek Tactical Simulator for the Atari2600 are favorites aswell.