So I be-bopped on over to Stage 6 and viewed their preview for the upcoming episode of Stargate: Atlantis.

My personal fanon is that John and Elizabeth used to be married. This explains how she trusts him to be her "man on the inside" in Rising when Sumner goes out looking for refuge. It's also a tidy explanation for him knowing her birthday in Before I Sleep (her surprise is at him knowing the particular jar she'd been coveting). It explains how they are so comfortable with each other so quickly in season one, and his confidence in his interpretation of her wishes when Rodney and Keller save Elizabeth using nanites. It is not contradicted in Sunday, where John tells Ronon that he was married before.

This fanon is about to be completely Jossed to hell and gone.

*pout*