Caution: Spoilers!

I recently rewatched every River episode of Doctor Who in River-order. I have come to the following conclusions:

1. River is the daughter of Amy Pond and Rory Williams. When River encounters the Silence, she, like Amy, is plagued with stomach pains. It would be easy to assume, say, two pregnancies here. More significant, however, is the fact that here, Amy is probably pregnant, and a character heavily implied to be the daughter that she’s pregnant with is also present. Perhaps River experiences stomach pains because she is crossing her timestream twice at this juncture. Other supporting evidence includes the close relationship between River and Amy seen in A Time of Angels—it’s River, not the Doctor, who saves Amy in Flesh and Stone, and River seems to view Amy with an immediate fondness.
2. Amy’s daughter has some powers similar to those of a Time Lord because of time spent in the TARDIS (just as Amy feared). This would lead to her wibbly wobbly pregnancy test, as well as explain why she was afraid to tell Rory (as stated in the episode). Also her regenerative powers.
3. Rory is still significantly jealous of the Doctor and Amy’s friendship. What sort of reaction might he have when he learns that Amy’s child has some Time-Lord-esque powers?
4. The upcoming episode 7, is titled “A Good Man Goes to War,” and promises to feature the Doctor and Rory going on some sort of quest to save Amy. Rory has already been established as a good, faithful husband—waiting outside the Pandorica for 2000 years for Amy (swoon!). Could “a good man” refer to Rory and not the Doctor? Is the Doctor even “a good man”?
5. River killed “the best man she ever knew.” Again, could this refer to Rory?
6. It’s important to remember in all of this that in our first meeting with River, she tells us that she lies. Oh, and the Doctor, too. Many possible inconsistencies here—including the fact that she acts like she doesn’t know Rory upon initially meeting him—could be hand-waved away this way.
7. If Rory kills the Doctor in one timeline, it might give River license and reason to go back and pre-preemptively kill him. She shows a slavish dedication to the timeline’s consistency only insofar as it applies to her relationship with the Doctor (she doesn’t want him to rewrite “a single word”). If she already knows that she kills Rory, then she wouldn’t do anything to stop it from happening so long as it ensures that her relationship with the Doctor will remain intact. 
8. We know that Amy’s daughter stays with her long enough to have at least one picture taken with her.
9. What River says about the Doctor always appearing in reverse order from her is true so far with two exceptions: 1. The appearance of Future!Doctor in The Impossible Astronaut 2. In the significant gap of time between Flesh and Stone and Silence in the Library. During that time period, River is released from Stormcage, becomes a Professor, is relocated to a time almost one century previous to her time in Stormcage, encounters a Doctor from much further along in his timeline who gives her his sonic. I’d imagine that a lot more happens in that time period that we’ll see in the future.
10. Anyway, ten points is nearly enough. In short, I think that Amy, Rory, and the TARDIS create a baby, who is somehow ill and displays Time Lord-like powers. Amy names her River, after River. Rory, believing that River is the Doctor’s daughter, kills the Doctor. A future!River, who is in love with, and possibly married to the Doctor, kills her father to ensure that her timeline with the Doctor will happen uninterrupted, and is imprisoned in Stormcage for this (probably by the Time Agency, for crimes against … time). Baby River is taken by the Silence to pilot their TARDIS, at which point she is shot at by mom, robbed of the suit that’s keeping her alive, and regenerates. She somehow travels into the future has a wild, somewhat promiscuous life (which she’s hinted at a bunch of times), becomes an archaeologist, marries someone with the surname Song, then probably divorces him. After, she meets the Doctor, who already knows everything about her. He gives her a list of meetings, asking her not to spoil anything for him. They fall in love, and marry. She encounters the Ponds, traveling with the Doctor, watches her father kill the Doctor, then premptively kills him.
11. Wibbly wobbly, timey wimey.