Okay, so the easiest way to do this is just to link to the journal entry that I read, and thank you very much hermitknut. Read everything, including the comments.
I went back and watched all of the scenes mentioned and did a little bit of poking around, and I'm pretty excited. That scene in Flesh and Stone caught me as odd; now it rings all sorts of alarm bells, and yeah, the jacket, and the watch... *flails* Same thing with the shadowy figure in The Eleventh Hour, omg. Same thing with the out-of-place sound bites in almost every ep. ...I'm even willing to believe that scene with wee!Amelia just before Amy wakes up at the end of The Eleventh Hour might be significant.
...*bouncy bounce bounce bounce* :DDD
In other news, speaking of complex plots I would like to unravel, why White Collar season finale horrible cliffhanger WHY. July cannot come fast enough. *fidget flail foam-at-the-mouth*