Based on the QS -World University rankings 2011/12, University Of Cambridge in London bagged the Top spot for 2 consecutive years followed by Harvard University. Only four schools from the philippines are in the top 700 and none of them made it to the top 200.

332 - University of the Philippines (ranked 314 in 2010 and 262 in 2009)
360 - Ateneo De Manila University  (ranked 307 in 2010 and 234 in 2009)
551 - 600   De La Salle University (ranked 451 - 500 in 2010 and 401-500 in 2009)
601+ University of Santo Tomas  (ranked 551 - 500 in 2010 and 501-500 in 2009)

Meanwhile, in the QS - Asian University rankings. Only 15 University was included in the list and only 4 University made it to the top 200 spot. Universities  from Hong kong grabbed  the top spot (The Hong Kong University of Science and Technology) and the second spot (University of Hong Kong) respectively 

62 - University of the Philippines
65 - Ateneo De Manila University
104 - University of SantoTomas
107 - De La Salle University

Other Universities  included in the 201+ ranking were as follows

Mapua Institute of Technology
PolytechnicUniversity of the Philippines
University of Southeastern Philippines
Central Mindanao University
Saint Louis University
Mindanao State University
University of San Carlos
Siliman University
Father Saturnino Urios College
Adamson University
Xavier University

for further readings regarding the methodologies used you may opt to visit the site below:
Topuniversities.com