Here's the obvious direction they could be going with Boomer (which I think would be rather neat):
Remember way back in "Downloaded", when Caprica Six mentioned to Boomer that she personally got the Colonial defense codes from Baltar? Well, what if the Cylons decide they want to try Boomer for betraying them, and then Boomer retorts with someone along the lines of "Hey, you want to punish me for going along with Cavil's attack on you? Why can't you be as forgiving as the humans, who've apparently let Baltar and Caprica Six off scot free, despite their being the ones most directly involved in the attack on the colonies?"
And then all the humans would respond with "What?!? Baltar was involved in the attack on the Colonies? Caprica Six was the one who personally hacked our defenses? They must pay!!!" (Remember, Roslin is the only other human who knows about Baltar's complicity in the attacks, and *none* of them know about Caprica Six's role.)
This could set up an interesting showdown with Baltar's cult.....and could also blow apart the Colonial/Cylon alliance, if the Colonials suddenly realize that the *one* Cylon most responsible for the genocide (Caprica Six) is right there on Galactica.
Also, I just realized that the fact that none of the Colonials knows about Caprica Six's involvement in the attack on the Colonies makes the fact that they all call her "Caprica Six" that much more ridiculous. Why the frak would they call her "Caprica Six"?