I would normally link to Dave Wrote This instead of giving the URL of http://davewrotethis.blogspot.com/2011/10/announcing-noughties-blogfest.html, but alas I am updating from work due to lack of proper planning on my part. The image would also normally by hyperlinked and probably will get that treatment in the near future. Enough excuses from me; on to the list. 
I will be listing what I believe was the best Science Fiction/Fantasy/Horror film or book for each year.
2000- You know Pitch Black came out of nowhere to be way cooler than a really cool, waited for it all my life X-Men movie, Fantasy would be Crouching Tiger Hidden Dragon, and over in Japan a little movie called Ju On was making waves in the horror genre. Book-I Think A Deepness in the Sky just slips past Cryptonomicon.
2001- Donnie Darko fits all categories on movie, special mention to Spirited Away. Book- I am tempted to give it Martin and his Song of Ice and Fire entry, but Clarke gets an honorary for 2001 here.
2002- Equilibrium, is the Sci-Fi film of the year, but look for Imposter as well. Fantasy- LOTR; TTT. Horror Bubba Hotep. Book- I think American Gods does a pretty good job representing this year.
2003- Not a great year, But X2 tops the list for SciFi. Fantasy-Big Fish, hands down. Horror-It wasn’t an awesome year hear and I have not seen Wrong Turn, but that is considered the best on offer. Books-I say you go with Kiln People by David Brin.
2004- Spiderman 2, but I almost went with Eternal Sunshine… or Butterfly Effect. Fantasy- House of Flying Daggers. Horror- Goes to the Dawn of the Dead Remake and special guest star of Infection a Japanese movie. Book- Jonathan Strange and Mr. Norrell, hands down.
2005- Serenity. Fantasy-Mirror Mask. Horror- The Descent. Book-HP Half Blood Prince, but I am reading Never Let Me Go right now, so…
2006- Children of Men, Fantasy- Pan’s Labyrinth, Horror- The Host (Korean). Book Old Man’s War, by John Scalzi
2007- The Last Mimzy. Fantasy-300, pure awesome. Horror-Grindhouse double feature. Book-World War Z, Max Brooks.
2008- It wasn’t Tokyo Gore Police, but might be Iron Man. Fantasy-The Tale of Despereaux. Horror-Let the Right One In. Book-. Anathem, Neal Stephenson
2009- Moon. Fantasy-The Lovely Bones. Horror-Drag Me to Hell but also watch The Orphan. Book- The Wind Up Girl, Bacigalupi, really the best book of the year, in my opinion.
Hope you enjoyed the list. I haven’t seen or read everything and welcome your input on glaring omissions.