My favourite piece has to be Worthy of Survival. I see it mentioned once or twice on this list but it's not a "big hit" like with Storming of New Caprica, Wander my Friends or Prelude to War.
I presume all of you (us, now I've registered) here have the collections. There's a bit I'm referring to which stirs me more than any other: at 1:54. The strings.
You see, one of my favourite episodes is Exodus (dur :p) and there's a bit in the episode just when the Pegasus appears and Lee comes over the comms saying "Galactica, Pegasus; let us take some of this work off your hands" - and in the background it's the same part of music. This part of the score was not part of the piece Storming of New Caprica.
I love SoNC to bits (in fact, I often sit there playing it at work - I work a night shift with not a lot to do - with pots and pans and whatever I can find

) but that bit missing annoyed me. However, I discovered Worthy of Survival which is a nearly-4-minute piece of that small part of the score. Made me happy!!
I see you read this forum occasionally, Bear. Rather than e-mail you directly, as I'm sure you get a lot of e-mails, I'd like to take this opportunity to thank you for your hard work and skills - along with all of the instrumentalists and musicians who took part in the series and sound-tracks.
I used to play the Clarinet - but have not done so in years. I have an old recorder from school which I still keep with me and sometimes play along to your music when I listen to it. However, it's rather limited in the notes it can produce by its very nature. It's thanks to you - you, Bear - that I have on order a Yamaha B flat clarinet from e-bay. I'm intending to take up my old habits purely so I can actually reproduce (most of) the range of notes that your pieces deserve. I'm a little rusty, but give me a couple of months, I'll make a badly recorded version for you to (not) listen to

Thank you so much again.
EDIT: My other favourites are:
Something Dark is Coming
Pegasus
Martial Law
Gentle Execution
Roslin and Adama
1 Year Later
Battlestar Sonatica
Reading above, it's no wonder I like GE and SDiC, heh.