There were some throwaway lines I thought were interesting in their implications. On a baseship, one of the Sixes remarks that she finds it sad that the centurions don't understand "what we're doing for them." So, I guess that ties in with the motivations of the bulk of Cylon society (minus the Ones) for the attack, namely a paralyzing fear of humans. But I'm really interested in the idea that at least some of the humanoid models felt protective of the Centurions. And it ties in with what Natalie did later on. Maybe the Sixes had been looking for an excuse to liberate the Centurions the whole time.
One of the things the hybrid says during the attack is (thank you, BSWiki), "Nuclear devices activated, and the machine keeps pushing time through the cogs, like paste into strings into paste again, and only the machine keeps using time to make time to make time." Seems to me, this is referring to the cycle of time and the catastrophes on Earth and Kobol, and that "the machine" would, logically, be God (or the Third Party as a whole). So there's a point to anyone who had "God/The Angels/The Lords of Kobol are an even earlier iteration of the Cylons" in the pool.
When Fleet-Cavil first meets Fleet-Simon, he mentions how useless his team is, remarking that Fleet-Leoban was a yoga instructor, Tough-Six was a hooker, and mentions that "a Five on this ship" was the only one in a position to do any damage during the attack, but he screwed it up. Which leads to the question, what would
the first copy of Doral have done during the miniseries to disrupt the Fleet's escape if Baltar hadn't exposed him?
I'm also curious about what happened to Caprica-Cavil between meeting Six and being found by Anders' group. Did he download and return later, or ride out the attack on Caprica and then meet up with the occupation force, or what?
Also, just a point, it was interesting to see that, for Ellen Tigh, "In the airport headed home," is code for "In a nightclub at lunchtime trying to nail a celibate priest old enough to be her father." Sure, you could look at that as a continuity error, but that ignores the fact that before (and a few times after) her download, Ellen was a huge lying bitch.