My mainly Nintendo-slanted list, but please post your own lists!
1. Nintendo whoring out their characters to third parties
Who thought this was a good idea? The only game it seemed to help was Soul Calibur 2, which featured Link. Putting Mario, Luigi and Princess in EA games just cheapened their appeal, at least for me. Please, let's not do that again. I'm not even okay if Sonic & pals are in the new SSBM. No more.
2. Original Twilight Princess unveiling at E3
Now THAT was a real surprise. I don't remember if anyone was predicting it, but I sure didn't expect it. The audience reaction alone (cheers and crying) made it memorable.
3. Next-gen Zelda goes cel-shaded
Now THAT... yeah. Big surprise, no one ever expected it. Not much else to say.
4. Microsoft actually doing well
I don't think anyone expected Microsoft to actually place 2nd worldwide. I mean, the name alone made me think it would fail. That Tao Fang fighting game... Blinx? The Japanese pointing fingers and laughing? It all didn't matter. Came down to Halo and some great third-party titles.
5. Nintendo DS actually doing well
I'm the biggest Nintendo fan there is, and even I had reservations towards DS. It's just one of those things... once you get your hands on it, you get it, and you love it. Plus all the amazing games Nintendo's putting out helps.
6. Original Capcom 5
Yeah, let's not get into too much detail, but at the time it was a pretty big deal. Quite a surprise to most.
7. Metal Gear Solid on GameCube
Another surprise with a so-so ending. Kojima / Dyack / Miyamoto, wow! Should be an amazing experience, right? Some sloppy coding and really... just didn't feel like Kojima touched it. Still a fun game though.
8. GameCube/GBA Connectivity
I think we were all surprised that Nintendo thoughti t was a good idea to make people not only buy a GameCube and a game, but also Game Boy Advances to play it the "way it's meant to be played". Thankfully it failed.