I know it isn't in the running, but
The Legend of Zelda: Four Swords Adventures was my favourite game of this year.

Paper Mario TTYD.

It's gotta be Halo 2 for me. While I was still at the absolute nadir of my interest in gaming, Halo was the biggest part of my gaming experience in the first half of the 00s, and Halo 2 was a big deal for me. It was the first game I ever went to the midnight release for, and while I didn't like it as much as Halo CE, it was still an incredibly fun experience. The LAN days did give way to playing on XBL, and there was problems with cheaters on that, but several of the people I still play online with today I first met back on Halo 2. I still play the Campaign missions every now and then.

Damn, I thought Tropico released much earlier than that. Would have gotten into my top 5 otherwise.

Loved the first one, the second one was weird and i's difficulty went from easy-peasy directly to impossible with little in-between, the third one was wayyy too easy due to the introduction of oil, haven't played the fourth one and only had a quick look at the fifth.

Either way, I'll go with HL2 in the runoff

Halo 2 had my initial vote but since it somehow didn't make the runoff, World of Warcraft has my vote this time around. I was constantly switching between Halo 2 and WoW at the end of 2004.

What a great year for games in general. Half-Life 2 and Paper Mario TTYD I also loved. 

Since this thread is coming towards an end I would like to thank LiquidLaser for creating these game of the year polls.
The selection of their estimates for the favourite games of the year has generally been very good and the introductory descriptions of them have been interesting. Their other section has been carefully updated with the votes counted as best as possible, and their format with the runoffs has been novel and engaging. Thank you for doing this. It has been great to read most of the responses and think about my favourites again.

The polls have been by far my main reason for actively engaging on vgchartz again. This is great content.

The leading category before the runoff vote was actually "Other", but after doing the runoff vote, the top 2 games from the main poll stayed the same.  The 2004 Game of the Year is Half-Life 2 and the runner up is World of Warcraft.

This is the first year that both spots went to PC games.  I also think it will likely be the last.  This time period kind of marks the end of the era for big name PC exclusives.  Almost all of the big PC game developers got roped into console gaming going forward.  This year is PC gaming's way of going out with a bang.

Depending on what year you put Minecraft in, 2009 when it was first made public, or 2011, when it was "officially" launched (though at that point it wasn't PC exclusive anymore), that could be the one that wins.

Not that PC won't have some really great exclusives going forward, but yeah, generally speaking, most PC devs and publishers went multiplatform, some with OG XBOX, like Bethesda and Bioware, some few years later with PS360, so really slim chances of PC exclusive winning again for quite some time (unless VG Chartz harbours secret cults of ARMA, Witcher 1, STALKER: Shadow of Chernobyl, SPORE, Machinarium or something like that).

2009 had Demon Souls come out, 2011 Dark Souls, Minecraft will have stiff competition in either year.
Minecraft is really big, yet the term souls like is even bigger, gets thrown around all the time.

Stalker vs Bioshock / Uncharted / Super Mario Galaxy. Not a chance.

There's League of Legends and Roblox that are huge on PC, doubt they'll gain much traction here.

Yeah, as I said, unless there are some secret fan clubs around here for some of those PC exclusives, there are extremely slim chances that any of them will be even close to winning.

As for Minecraft - honestly, I'd take Souls anytime over it, but being the best-selling game of all time (by a quite a wide margin), Minecraft is almost in a league on its own, anyway you look at it.