Hm, I honestly, don't know how to vote, since I haven't voted for any of them as the best from their years.

I don't find any of them to be particularly at the spearhead of innovation, more of refinements to existing ideas, so I can't really pick based on that.
Also, I don't see a clear winner for most influential, so I can't use that criteria either.
I don't want to use what I'd replay the most, since that would be favouritism.
Using d10 roll to determine my vote would be silly as well.

So I guess I'm abstaining.

It's either Metroid Prime or Super Mario Galaxy for me, with Jak 3 and Kingdom Heartsjust a tiny bit behind them

Super Mario Galaxy was a lot of fun, and I honestly think the sequel might have been even better again.
However Metroid Prime gave me a great experience that I don’t remember feeling since. I don’t think I voted for Metroid Prime during that poll, but it claims my vote out of these 10 community chosen nominees.

Star Wars Knights of the Old Republic.

Of those I voted for Knights of the Old Republic, Zelda Twilight Princess, Mario Galaxy and Uncharted 2 in the threads. All great and all among my favourites, but Knights of the Old Republic is the easy winner. That game is basically perfect if you asked me.

I do think Playstation fans are underrepresented in the poll for this decade.  Yes, this site does slant toward Nintendo games, but there are PC games in the poll above.  Oddly enough there are also OG XBox games in the poll above.  I want to say that bad luck kind of played a role in the PS2, especially, getting shut out of the poll.  FF X, GTA 3, Shadow of the Colossus, etc... all got a lot of votes, but none of them managed to pull off a win.  The best PS2 games had tough competition each year, often against other PS2 games.  And while I'm sure KOTOR is a great game, no one really believes that people on this site are biased toward XBox.  It just had easy competition in its year, while all of the best PS2 candidates had tough competition and some very narrow losses.

Anyway, I hope Playstation fans can find something in the poll that they like, even if they aren't the biggest Uncharted fans.

This is cruel. Three of those games are in my top 10.

This is really splitting hairs, but it’s Halo. Still the height of the series for me, due to its amazing single-player campaign.

Second place would be Resident Evil 4, and third place Half-Life 2.

Resident Evil 4

It's one of very few games that I can find to fault with. Every single thing about it is amazing, from its white-knuckle action to its desolate atmosphere to its pitch perfect pacing, and it all gels together to create an experience like no other.
It effortlessly manages to top itself over and over, building from one thrilling encounter to the next like a symphony of adrenaline.
It's not just the finest game of the 2000s, but one of the greatest games of all time.

Although my highest rated game of the 2000s is ICO, the first on my list from this poll is

I was torn between metroid prime and resident evil 4. In the end I went with resident evil 4.

Have to go with Galaxy. While I love Metroid Prime and RE4, it took until they got Wiimote pointer controls for them to really click with me. Going by pure impact on the industry it's neck and neck between Halo and RE4, as each defined what console first person and third-person shooters became, respectively. But RE4 is far and away the better game of the 2 in my opinion since even with keyboard and mouse controls Halo 3 was the only game in the franchise that I felt was truly great and even that isn't one of my favorite games ever. If this was 2010 I'd have gone with Twilight Princess, but since Skyward Sword and Breath of the Wild I've found TP to have aged somewhat. It's still great, but no longer my favorite game of all time. Galaxy, meanwhile, is just as amazing as ever.