Freespace 1 was the first I played, and I couldn't get enough of it. From the beginning, I was intrigued by the story. The beginning movie, in Ross 128 really pulled me into the game. I'm just flying though, blasting Vasudans, and WHAMMO, scary red ships jump in, and destroy the Vasudans! I'm just about to say thanks, and then they jump out. I just shrug, and fly back to the Plato. Then, lo! Our friends come back! Crap, they just blew up the Plato. RUN FOR IT.
Playing Judas used to really thrill me, and I used to try as hard as I could to avoid getting pulverized by the Lucifer's fighters. (Before I knew that it was scripted.)
Freespace 2 was great, too. I was dissapointed somewhat that I was killing other humans, but then, woohoo! More badass Shivans!
Although, Freespace really made me think of the Shivans as the Great Destroyed, rather than omnipotent aliens who can't die. The Lucifer was INVULNERABLE, until the last second, and then you really fcked the human race by isolating their home planet.
What I mean by the Great Destroyed was, when you went against a Sathanas, all you had to do was take down FOUR beam turrets, and you WIN AT LIFE. Really not that hard. The flak and AAA hardly bother you. The Lucy, though, you had to take down five reactors in a time space of about 10 minutes in a hulky bomber with no shields. Not to mention the great Delta Serpentis footrace to get to the node.
FS1 takes the book for me, but if FS2 was still memorable.