• How does River know the Doctor’s name?
• Who blew up the TARDIS?
• Why does the (older) Doctor invite the Pond family (and himself) to Lake Silencio?
• Why does River not remember being the little girl in the astronaut’s suit?
• Who is Madame Kovarian’s boss?
• If that was the Doctor’s cot, why did he have it in the TARDIS?
• Who were Mels’ parents or guardians in Leadworth? (great question from @lone_locust)
• How did Mels get to Leadworth in the 1990s?
• Why wasn’t Mels at Rory and Amy’s wedding?
• How was River at Rory and Amy’s wedding?
• Did the Doctor revisit Rory and Amy’s wedding after River kissed him with her toxic lipstick, and before she saved him with her spare regenerations? (And if not, why the top hat and tails?)
• What did the Doctor whisper to River when he was dying?
• Doctor Who?
• What do Time Lords pray to?

• Who is the little girl who regenerated? (River)
• Who kills the Doctor? (River)
• What is the question hidden in plain sight? (Doctor Who?)
• Who did the Doctor see in room 11? (The Doctor)

Have I missed any?

Update 22:55 I missed some.
https://twitter.com/#!/lone_locust/status/119526564546355201

Also

• When was Amy swapped with her ganger?
• Who could project the signal to control the flesh through time and space into the TARDIS? (may be same answer as fifth question above)

Have I missed any more?

Update 1/10 12:20

Another thought: what actually kills the Doctor? What is that green flash? A weapon or a phenomenon, eg. the energy discharge from the shorting out of some time differential?