Personally, I think it was a tie inbetween Sony and Nintendo this year. For me personally, Sony stole the show, but that's because it's content was more aimed towards the games I like to play. However Nintendo hit all of it's high notes outside of Mario in one show, and I recognize it probably won in most ppl's eyes on Zelda, Metroid, and the 3DS alone.
As for Sony's show itself personally I thought it was an A show. Not perfect by any means, but they showed plenty of content, and did what they needed to. They showed off motion control games that actually looked fun. Showed off new exclusive titles and content. Gave live demos of upcoming big games like Killzone and LBP. Talked about the premium service (which isn't a big deal to me, but I'm sure it is to quite a few ppl). Gave release dates, and price ranges. They were also humorous and not creepy (see little girl yelling skittles for 5 minutes). Then gave (IMO) the only real shocker of E3. Which would be Gabe Newell eating crow on a Sony stage....I mean in Twisted Metal

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There were disappointing parts tho. No Last Guardian, or Team Ico collection talk. No DC Online or FFXIV release dates or beta info. No PSP 2. However I think the good points outshined what didn't make it into the show (plus TGS could always rectify those along with FFvsXIII).
As for what stood out, Twisted Metal easily. I've really, really been wanting another Twisted Metal, especially one in the same vein as Black, and we're getting it. Kevin Butler's speech was epic lol. Gabe showing up on a Sony show after all the crap he's spewed this entire gen made the show worth it by itself. Dead Space 2 gameplay was awesome. Also, Move finally selling me on the games. See, beforehand Move only had sold me on the hardware itself. The Engadget tech demos alone had me convinced to buy Move just based on what they were doing with it. Still tho there was a nagging feeling about it being tons of shovelware. This E3 showed it's not just shovelware + Socom, but an actual attempt to make somewhat more hardcore games with it, or make current hardcore games compatible with it.
So overall E3 in general is a win for me this year (I only watch the big 3). Microsoft dragged things down early on, but Nintendo and Sony raised it back up IMO.