Ok, here is a re-vamped list I have been working on throughout the night. It has been expanded with recent (near)masterpieces I've seen at this year's Berlinale for example, and I have also included many of the previous contenders, from the runners-up list in the next post. I might not have seen some of them for some years, but when i did I fell in love with them. So until I see them again, they will definitely stay in. 
Some other films which have been revisited and found "unworthy" (what a harsh term...) have been excluded (e.g. 5x2). 
As you can see I'm a bit uninformed from 2004/05 onwards, but hey, let's see your lists! (especially arsaib who offered such an extensive "best of 2005" recently "> ). 

Best of the Decade (So Far) 

2000 
Baise-moi *%#@ Me (Virginie Despentes, Coralie / France) 
Batoru rowaiaru Battle Royale [director`s cut] (Kinji Fukasaku / Japan) 
Before Night Falls (Julian Schnabel / USA) 
Cast Away (Robert Zemeckis / USA) 
Code inconnu: Recit incomplet de divers voyages Code Unknown (Michael Haneke / France, Germany, Romania) 
Die Polizistin The Policewoman (Andreas Dresen / Germany) 
Djomeh (Hassan Yektapanah / Iran, France) 
England! (Achim von Borries / Germany) 
Eureka (Shinji Aoyama / Japan) 
L'amour, l'argent, l'amour Love, Money, Love (Philip Groning / Germany, Switzerland, France) 
La ville est tranquille The town is quiet (Robert Guediguian / France) 
Maelstrom Maelstrom (Denis Villeneuve / Canada) 
Proof of Life (Taylor Hackford / USA) 
Sanger fran andra vaningen Songs from the Second Floor (Roy Andersson / Sweden, Norway, Denmark) 
Shadow of the Vampire (E. Elias Merhige / UK, USA, Luxembourg) 
Shiqi sui de dan che Beijing Bicycle (Xiaoshuai Wang / China, Taiwan) 
Soins et beauté (Alejandra Rojo / France) 
Sous le sable Under the Sand (Francois Ozon / France) 
Takhte siah Blackboards (Samira Makhmalbaf / Iran, Italy, Japan) 
The Claim (Michael Winterbottom / UK, France, Canada) 
The Heart of the World (Guy Maddin / Canada) 
The Million Dollar Hotel (Wim Wenders / USA, Germany, UK) 
Unbreakable (M. Night Shyamalan / USA) 
Uttara (Buddhadev Dasgupta / India) 
Zhantai Platform (Zhang Ke Jia / China, Hong Kong, Japan, France) 

2001 
Akai hashi no shita no nurui mizu Warm Water Under a Red Bridge (Shohei Imamura / Japan) 
Atanarjuat The Fast Runner (Zacharias Kunuk / Canada) 
Avalon (Mamoru Oshii / Poland, Japan) 
Das Experiment The Experiment (Oliver Hirschbiegel / Germany) 
Der Felsen A Map of the Heart (Dominik Graf / Germany) 
Enemy at the Gates (Jean-Jacques Annaud / USA, Germany, UK, Ireland) 
Freunde The Whiz Kids (Jan Kruger, Oliver Schwabe (co-director) / Germany) 
Je rentre a la maison I'm going Home (Manoel de Oliveira / France, Portugal) 
La Pianiste The Piano Player (Michael Haneke / France, Austria) 
Monster's Ball (Marc Forster / USA, Canada) 
Mulholland Dr. (David Lynch / USA, France) 
Nichts bereuen No Regrets (Benjamin Quabeck / Germany) 
Sen to Chihiro no kamikakushi Spirited Away (Hayao Miyazaki / Japan) 
The Royal Tenenbaums (Wes Anderson / USA) 
Tu vois (Francois Ruiz / France) 
Unloved (Kunitoshi Manda / Japan) 

2002 
8 femmes 8 Women (Francois Ozon / France, Italy) 
25th Hour (Spike Lee / USA) 
About Time 2 (Mike Figgis / USA) 
Adaptation. (Spike Jonze / USA) 
Bungalow (Ulrich Kohler / Germany) 
Catch me if you can (Steven Spielberg / USA) 
Changing Lanes (Roger Michell / USA) 
Dans le noir du temps (Jean-Luc Godard / France) 
Dolls (Takeshi Kitano / Japan) 
Elsker dig for evigt Open Hearts (Susanne Bier / Denmark) 
Hable con ella Talk to Her (Pedro Almodvar / Spain) 
Heaven (Tom Tykwer / Germany, Italy, USA, France, UK) 
Kôfuku no kane Blessing Bell (Sabu / Japan) 
Lanse da men Blue Gate Crossing (Chin-yen Yee / Taiwan, France) 
Le fils The Son (Jean-Pierre & Luc Dardenne / Belgium, France) 
Madrid (Daphne Charizani / Germany) 
Nebo. Samolyot. Devushka. Sky. Plane. Girl. (Vera Storozheva / Russia) 
Nuomos sutartis The Lease (Kristijonas Vildziunas / Lithuania) 
Punch-Drunk Love (Paul Thomas Anderson / USA) 
Shin jingi no hakaba Graveyard of Honor (Takashi Miike / Japan) 
Sophiiiie! (Michael Hofmann / Germany) 
The Hours (Stephen Daldry / USA) 
Uzak Distant (Nuri Bilge Ceylan / Turkey) 
Vendredi Soir Friday Night (Claire Denis / France) 
White Oleander (Peter Kosminsky / USA, Germany) 
Xiao cheng zhi chun Springtime in a small Town (Tian Zhuangzhuang / China, Hong Kong, France, Netherlands) 
Ying xiong Hero (2002 / Zhang Yimou / China, Hong Kong) 

2003 
21 Grams (Alejandro Gonzalez Inarritu / USA) 
Bu jian The Missing (Lee Kang-sheng / Taiwan) 
Bu san Good Bye, Dragon Inn (Ming-liang Tsai / Taiwan) 
Dogville (Lars von Trier / Denmark, Sweden, UK, USA, Germany, Finland, Netherlands, France, Norway) 
Elephant (Gus Van Sant / USA) 
Goff in der Wuste Goff in the Desert (Heinz Emigholz / Germany) 
Histoire de Marie et Julien The Story of Marie and Julien (Jacques Rivette / France, Italy) 
Identity Kills (Soren Voigt / Germany) 
L'esquive Games of Love and Chance (Abdellatif Kechiche / France) 
Lichter Flickering Lights (Hans-Christian Schmid / Germany) 
My Life Without Me (Isabel Coixet / Spain, Canada) 
Noi albinoi Noi the Albino (Dagur Kari / Iceland, Germany, UK, Denmark) 
Open Range (Kevin Costner / USA) 
Raja (Jacques Doillon / Morocco, France) 
Schussangst Gun-shy (Dito Tsintsadze / Germany) 
Son frere His Brother (Patrice Chereau / France) 
Te doy mis ojos Take my eyes (Iciar Bollain / Spain) 
The Brown Bunny (Vincent Gallo / USA) 
The Station Agent (Thomas McCarthy / USA) 
Wonderful Days (Moon-saeng Kim / South Korea) 

2004 
Before Sunset (Richard Linklater / USA) 
Birth (Jonathan Glazer / USA) 
Dare mo shiranai Nobody Knows (Hirokazu Koreeda / Japan) 
Eternal Sunshine of the Spotless Mind (Michel Gondry / USA) 
Frau fährt, Mann schläft (Rudolf Thome / Germany) 
Gegen die Wand Head-On (Fatih Akin / Germany, Turkey) 
Le chiavi di casa The Keys to the House (Gianni Amelio / Italy, France, Germany) 
Le conseguenze dell'amore The Consequences of Love (Paolo Sorrentino / Italy) 
Marseille (Angela Schanelec / Germany) 
Shi mian mai fu House of Flying Daggers (Zhang Yimou / China, Hong Kong) 
Sud pralad Tropical Malady (Apichatpong Weerasethakul / Thailand, France, Germany, Italy) 
The Aviator (Martin Scorsese / USA, Japan, Germany) 
The Life Aquatic with Steve Zissou (Wes Anderson / USA) 
Tony Takitani (Jun Ichikawa / Japan) 
Trilogia I: To Livadi pou dakryzei Trilogy: The Weeping Meadow (Theo Angelopoulos / Greece, Germany, France, Italy) 

2005 
...Es wird jemand kommen, der ja zu mir sagt Ruth (Michael Blume / Germany) 
Amour neutre Love neutral (Pierre Coulibeuf / France) 
Au-dela de la haine Beyond Hatred (Olivier Meyrou / France) 
Babooska (Tizza Covi, Rainer Frimmel / Italy, Austria) 
Batalla en el cielo Battle in Heaven (Carlos Reygadas / Mexico, Belgium France, Germany) 
Broken Flowers (Jim Jarmusch / USA, France) 
Cache Hidden (Michael Haneke / France, Austria, Germany, Italy) 
Invisible Waves (Pen-Ek Ratanaruang / Thailand, Netherlands, Hong Kong, South Korea) 
Kaalpurush Memories in the Mist (Buddhadev Dasgupta / India) 
Mizu no hana Water Flower (Yusuke Kinoshita / Japan) 
Nekam Achat Mishtey Eynay Avenge but One of my Two Eyes (Avi Mograbi / Israel, France) 
The New World (Terrence Malick / USA) 

2006 
46-okunen no koi Big Bang Love, Juvenile A (Takashi Miike / Japan) 
Aus der Ferne "From far away" (Thomas Arslan / Germany) 
Bamako (Abderrahmane Sissako / Mali, USA, France) 
Il regista di matrimoni The Wedding Director (Marco Bellocchio / Italy) 
In Between Days (So Yong Kim / Canada, USA) 
La-bas Down There (Chantal Akerman / Belgium, France) 
La science des reves Science of Sleep (Michel Gondry / France, Italy) 
Lady Chatterley (Pascale Ferran / France, Belgium) 

2007 
State Legislature (Frederick Wiseman / USA) 


Number of Films by Country: 

USA: 30 
France: 20 
Germany: 20 
Japan: 13 
Canada: 5 
China: 5 
Italy: 4 
Taiwan: 3 
Belgium: 2 
Denmark: 2 
India: 2 
Iran: 2 
Spain: 2 
Thailand: 2 
UK: 2 
Greece: 1 
Iceland: 1 
Israel: 1 
Lithuania: 1 
Mali: 1 
Mexico: 1 
Russia: 1 
South Korea: 1 
Sweden: 1 
Turkey: 1 
_______________ 

Total: 124 

* added Frederick Wiseman's cinematic poem State Legislature as well as Avi Mograbi's wonderfully compelling and personal documentary-essay "Avenge but One of my Two Eyes". Also kicked out Christopher Nolan's Memento after a re-watch and included Chin-yen Yee's "Blue Gate Crossing" (2002)