First of all, I think it's worth noting that people seemed to think that Sony won that year. But seeing how these threads are focusing on a publisher basis as opposed to a platform basis, I have to give it to Sega.

Let's look at the games they were showing that year. You've got well-regardedclassics like Chu Chu Rocket, Jet Grind Radio, NBA 2K1, NFL 2K1, Phantasy Star Online, Samba de Amigo, Seaman, Shenmue, Skies of Arcadia, Sonic Adventure 2, Space Channel 5, and Virtua Tennis, along with some less-remembered but then-acclaimed games like F355 Challenge, Headhunter, Metropolis Street Racer. That's a total of about 15 games, and unlike some companies nowadays that show their games half a decade before they're released, most of them were available before the end of 2000. That's one of the densest ever eras of high quality releases from a first party publisher in gaming history.

I know it's only two games but it's hard to top Diablo II and Warcraft III so it's Blizzard for me.

I went With Sega even though I haven't played that many of the games but I remember really enjoying Jet set radio. From my perception all games are still loved by its fans even if they were not all big seller (Maybe not space channel 5 not sure about that one).

From my personal bias both Nintendo and blizzard have most of the games I care a lot about today. Also a bit fun seeing several games from EA that I have fond memories of as there is not that much from them that matches my gaming taste nowadays. Even though I think The world is not enough probably was a bad game but I liked bond even if it wasn't as good as Golden eye. But SSX and Command & Conquer: Red Alert 2/Renegade were both really fun.

I loved the Command and Conquer games as a old kid/young teenager. Played those with my friends all the time.

Wow, this is a close one so far! Keep the votes coming!

They were so fun but I was incredibly bad at RTS games as a kid. But not that many of my friends were too good anyways so I could still enjoy it

Ok, so looks like this voting is really about software rather than hardware.  There is some close competition here.  These are the companies that stand out to me:

First the honorable mentions:
SEGA: Samba de Amigo, Space Channel 5, Seaman, Phantasy Star Online, Shenmue, Jet Set Radio
Blizzard: Diablo II, Warcraft III

This is a long list of games that I've heard great things about, but have never played.  If I had to guess which games I'd like better though I'd probably choose Blizzard over Sega.  I would like to get around to trying Diablo 2 and Warcraft 3 at some point.  Sega has a good list too, but it's more because of the quantity of games rather than 1 game that makes me super excited.

Anyway, here are my real contenders:
Sony:  Gran Turismo 2000, ICO, FantaVision, The Legend of Dragoon
Bioware: Baldur's Gate II, Neverwinter Nights
Squaresoft: Chrono Cross, Final Fantasy 9, Final Fantasy Online, Legend of Mana, Vagrant Story

Ok, so first there is Sony.  I normally don't think of them as top tier in software development, and I'm not much of a GT fan.  However, this year had both ICO and LoD.  That's an amazing year for Sony.  

Bioware is not a company I'm really interested in anymore, but in 2000 I played both BG2 and Neverwinter Nights.  Neverwinter Nights is one of my top 50 games of all time.  This was almost all that I played for at least a year, since it has this amazing tool set that let players create their own modules.  Most of these modules are only so-so, but the top votes ones are all amazing, and I had a ton of fun playing through all of the early ones.

Lastly, there is Squaresoft.  This is still in the late Sakaguchi era, which was when Squaresoft was at its peak.  Final Fantasy 9 and Final Fantasy Online are both in my top 50 games of all time.  Even though I played NWN for over a year, I played FF Online for 2-3 years.  And then there is FF9 which I would say is actually better than either of those games.  It's my second favorite FF, which is my favorite series.  The other 3 games are not games I've played yet, but they are all games that I would like to play someday.

Overall, I'd say 2000 was an awesome year for E3 with a lot of great reveals all around.  However, if I had to pick one winner, then it would be Squaresoft.  This was the era of their last few great years and it shows in their software lineup.

EDIT: I just noticed Squaresoft is not in the poll.  WTF?  Don't you know greatness when you see it.   Guess I have to pick Bioware?

Sadly the poll options are limited at 10. I try to do my best to figure out who should be in that list, but I can't be perfect. That being said I do track comment votes.

A good rule of thumb is to make option 10 "other" if you don't think there are enough options.