My list is quite a mixed bag and admittedly not an extensive one,but these movies IMO are among the most notable,if not the best,Filipino movies of the Noughties:
Tanging Yaman, by Laurice Guillen (2000)
Bagong Buwan, by Marilou Diaz-Abaya (2001)
Magnifico, by Maryo J. delos Reyes (2003)
Crying Ladies, by Mark Meilly (2003)
Panaghoy Sa Suba, by Cesar Montano (2004)
Ang Pagdadalaga Ni Maximo Oliveros, by Auraeus Solito (2005)
Masahista, by Brillante Mendoza (2005)
Kasal,Kasali,Kasalo, by Jose Javier Reyes (2006)
A Love Story, by Maryo J. Delos Reyes (2007)
One More Chance, by Cathy Garcia-Molina (2007)
Ploning, by Dante Nico Garcia (2008)