I agree with the third being the best. It had nice EGA graphics, and was the last one with the text interface. The full on Star Trek mode of part 5 was fantastic as well. I liked 4 but I didn't love the graphics which they seemed to try to go a little too digital with. If I recall it had voices and stuff but then 5 was off the CD-ROM and back into 3.5" disk mode. Seemed weird.
I loved all of them except for maybe 6 which I didn't get running well on release and didn't hold my interest when I tried it some years later. Maybe i'll give it another shot.
Also Roger Wilco, you should go back to your Roger Wilco av and ditch the pony crap