This is a thought that I came up with that I posted on another forum after ruminating for a while...
Ok, so let me first state that each dream sequence appears to vary and be tailored to each character you play? I've been watching clips to make sure I'm not crazy but they all differ. Anyways...
I've been thinking about the indoctrination theory, the dream sequences and the "godchild"/catalyst...and I thought...
In one of Shepard's dream sequences for my character, he does the typical running and what not. But there is a voice speaking to him. Someone or something saying "The enemy of my enemy...is my friend" or something to that effect. it's a bit unintelligible. I don't remember if there was any speaking in the dream before that, but it's a deep voice and sort of dark. You hear the same voice calling his name in the final dream sequence. Thinking even further into this subject, the voice sounds surprisingly and suspiciously close to Harbinger when you fought the collectors he had control over in ME2.
If the indoctrination theory is right, it would make sense. Since reapers can't directly suggest things to their indoctrinated thralls without turning them into vegetables, it would make sense that Shepard would hear Harbinger talk to him in his dreams which are more indirect and subliminal.
Just a thought. Going through my second play through I started thinking about it more in depth since the first playthrough I heard it, but didn't actually *listen* because I was still in awe and blown by all the events that had happened, and distracted by dialogue and what not.
Also, I stumbled upon this link going into more strange occurences in the game that suggest indoctrination as a possibility:
http://www.fanfiction.net/s/7920772/1/