Getting Sam and Jack together might be great for the fans, but it would seriously break a military taboo, which is why Jack kissed her after resigning during the time loop. If he did that beforehand while being her commanding officer, he'd be in front of a court martial so fast, both their heads would spin. I'm not certain that even if they weren't on the same team that such a union would be permitted under UCMJ since there is such as disparity in their ranks. On a show like Jag, that would be permitted since the two leads are of the same rank (Mac is a Lt. Colonel and Harm is a Commander) even though they work together because neither reports to the other.
So I doubt officially getting them together is in the cards. I think since Shaare/Amaunet (sp?) is gone, she'd make a good match for Daniel. Both are eggheads, able to talk geek for hours while Jack stands around with that baffled look on his face. I think that'd be great, especially since Daniel is a civilian. The UCMJ wouldn't forbid that.
