(spoilers) Complete list of foreshadowing:

[Mad Manny]

This story has some of the best foreshadowing I've ever encountered, I'm talking better than 6th sense or Fight Club!
For example the developer could have gone the easy route and completely hidden Ed's goal to get close with Anna at the subway, but instead they put it BLATANTLY in full sight having him say "it's now or never, come on.. talk to her" but it was so brilliantly executed that we were lead to believe that he was just trying to gather up the courage to talk to a hot girl, so when his true intentions were revealed I was just in shock at how I could have missed all the signs that were thrown right in my face!

I would be curious to see if we could compile a full list of all the foreshadowing, I'll start:
*(as I said) Ed's thoughts reveals his plan to talk to Anna on the subway.
  *And he even had knowledge that it was her stop. (I assumed he was just a bit creepy akward).
*The subway map clearly shows that Ed and Anna would not be on the same subway track on their way to work.
*Ed's apartment doesn't look like someone who's trying to meet girls, it looks like a hide-out for a evil mastermind.
*Ed leaning his head down in shame after some conversations (I forget which).
*The entire story starts out with Ed learning about the Uncles plans to ruin the research, that's a motive right there thrown in your face within the first couple of seconds.
*When you pick up the notepad in the vault I specifically saw with my own eyes that the extra "blame the cop"-note was NOT there when Ed had it, only when Anna received it, yet I STILL assumed that ray (who went in first) had put it there.
*Ed is blonde, blonde males are always evil in a cowardly fashion (or so Hollywood has taught me).

Can you think of any more?

(Btw also I REALLY apprieciate how rather than just revealing the twist in a cutscene he forced us to figure it out ourselves, it took me a while but it was worth it!)

[ChaiHai]

Thank you for your post. Now that I think about it, yes, it was foreshadowed, though not in the way you'd expect. I didn't catch the meanings behind any of them and was completely shocked. As a result, I felt betrayed by Ed, having been rooting for him the entire game.
I also enjoyed the false snakes that were thrown our way. The cop was my favorite of the four, and I didn't believe it for a second when he was accused. I also enjoyed the do not trust the reporter note. The game attempts to have us cast suspicion on the two characters who ultimately defeat the corporation and Ed. I liked Ray least of all, but I suspected him of no wrong doing, but I can see how others due to the note might have cast suspicion. 

[ZX497]

To add something, if you check the address book of Ed's phone at the start of the game, you'll find that the only number listed there is 14A, which is the number of the first resonance device.

[Mad Manny]

To add something, if you check the address book of Ed's phone at the start of the game, you'll find that the only number listed there is 14A, which is the number of the first resonance device.

Technically that may not foreshadowing, hmm unless I'm using the wrong word here, what I mean are clues that the player can use to figure out the twist before it has been presented, and since you only get the resonance device AFTER Ed came out of the closet I'm afraid that wouldn't count.

[ZX497]

Yeah, I suppose so. I think it adds up, though, you gotta admit it's a bit weird if the only listed address on a phone is something called "14A". Heck, he didn't even have Morales' number listed

Another thing that sort of adds up to Ed's motives, is the inner monologue he does if you use him to solve Morales' Journal during the magnet puzzle. It reveals Ed has been suspecting that Morales had been hiding things from him, and that Ed thinks he deserved more after all the work he's done for Morales.

[Mad Manny]

Another thing that sort of adds up to Ed's motives, is the inner monologue he does if you use him to solve Morales' Journal during the magnet puzzle. It reveals Ed has been suspecting that Morales had been hiding things from him, and that Ed thinks he deserved more after all the work he's done for Morales.

Cool, I didn't know of that one!

Which reminds me of YET another one:
*Ed said he had a metal shoulder which is why he should carry Bennet's gun in the big magnet puzzle, that sounded like an excuse to get a hold of a gun.

(the more I think about this game the more I like it )

[Rognik]

There's an optional clue during "Chapter 2." If you pass around the cotton swabs, everyone is willing to take a cheek sample to scan in Antevorta. However, Ed adamantly refuses to do so; if you try, he'll say "why would I want to do that?" Since the only reason to sample DNA is to scan in the Antevorta machine, it shows that he knows what it's all about and doesn't want to give them extra data.

[Castledoque]

However, Ed adamantly refuses to do so...

Wow, I hadn't seen that. Such an amazing carefully constructed game! It's details like that that never cease to amaze me. To think that people, like that reviewer at Gamespot, actually accuse it of sloppy writing...

[Mad Manny]

I just remembered yet another one:
In the hospital after the scientists death Ed reacts excessively cry-baby when he says he's sorry about the death, at the time I thought he was just a total cry-baby, now I realized his reaction wasn't an over-reaction at all; he had just committed his first MURDER and had to witness the victims daughter mourning the death, knowing that information makes his reaction sensible.

[snarky]

There are a few hints in the first scene:

- Ed says he can't wait to move out of his apartment. (What is he expecting?)
- For some reason, the night before he borrowed a tripod from his neighbor, calculated exactly where to place it, and marked the spot on the floor with masking tape.

Later on, he very clearly lies to the others about what Dr. Morales wanted to do with the resonance technology (he says they mustn't destroy it because Morales wanted it to benefit mankind, when in fact he had been planning to destroy it just before he died). And once you read Dr. Morales' journal, he's the primary suspect for having stolen the two missing resonance devices.

[VinceTwelve]

Wow, this is a great thread!  I'm really glad that people picked up on some of these things!  Super excited to read all the discussion on this forum (which I've been mostly just lurking).  Thanks!

It was important for me to have all these hints that might have one meaning the first time you play the game and another meaning on a second play through.  Glad to see it well received!

One other I'll add myself:

When Ray tries to join the group, Ed says something like "No more people!  It was just supposed to be Anna and me!"  His plan is spiraling a bit out of control at this point...  which will lead to the tragic event.