Oh man, there were so many...
--The Field of Battle really impressed me the first time I played it. Much fun.
--The Hammer and the Anvil had great atmosphere.
--So did Playing Judas. Nothing beats the "OH, CRAP!" moment when the Lucifer jumps in. Well, maybe the "You're kidding me!" moment when Command tells you to fly into the docking bay.
--Evangelist was fun.
--Exodus had great atmosphere and really captured the feeling of recovering after a massive attack.
--Black Omega was lots of fun. Take out a Typhon - whee!
--Good Luck goes without saying.
Those were the ones that stood out the most. Overall I'd say Playing Judas, Black Omega and Good Luck.