I'll bet that a big piece of the next season is getting into the origin of the humanoid Cylons. We don't really know where they came from. Were they derived from humans in the first place? Has there been much if any interaction between the Cylons (the major 7 or the mysterious 5) and the humans? What's with the two Cylon factions? And, what's up with the "plan" that's been mentioned in the title sequence for each and every episode? What, exactly, is the Cylon plan?

So far as I can tell, all of the mysteries set up at the end of Season 3 are designed to set up these sorts of questions being answered in Season 4.