Not quite sure what you're asking here.
Who had the best conference? Ubisoft, even though I really didn't care for the hosts. They showed off great games, had a few big announcements, and generally stole the show.
Who is currently winning E3? That's a different matter. I generally like to think that it's the gamers who truly win E3, but so far that isn't the case this year. It certainly isn't the case for Wii and Vita gamers. The current winner of E3 is disappointing, because they didn't show off a single game. They didn't even have to show up to win. They're getting software support from Microsoft, Sony, AND Nintendo. The true winners are the mobile platform providers. Apple. Google. Technically Microsoft could be included, but let's face it: they're not exactly sweeping the competition in the mobile department, which is why their service will run on all mobile devices, not just their own.
Since that answer feels like cheating, I believe that of the big three, Sony is currently having the best E3. I believe that Nintendo has presented better material, but that expectations were (rightly) higher for Nintendo than for Sony, and Nintendo has failed to meet those expectations.
However, E3 is far from over. If Nintendo has a couple of nice announcements planned for their software conference tomorrow, they could quickly steal the show back. Sony has made it easy for them by effectively ignoring the Vita.
However, if any individual console is currently "winning" E3, it's the PS3, and that's unlikely to change no matter what Nintendo announces for 3DS tomorrow. Only an unfathomably unlikely surprise last-minute megaton announcement could upset the PS3's position.