I tried tallying the votes from this poll (though I admit it's not fool-proof), and the results were quite instructive. It should be noted that I considered only those votes submitted in response to this particular poll, hence those lifted from Joel David's book and QTV's Ang Pinaka- (just to cite some examples) were not counted. The respondents ranged from industry professionals to film critics to pinoydvd.com members.
The top ten (in ascending order): Scorpio Nights, Itim, Biyaya Ng Lupa, Tinimbang Ka Ngunit Kulang, Insiang/Himala (tied), Oro,Plata,Mata, Kisapmata, City After Dark, Maynila Sa Mga Kuko Ng Liwanag.
So that's 3 by Lino Brocka, 2 each by Ishmael Bernal, Mike De Leon, and Peque Gallaga, and 1 from Manuel Silos. Brocka also has the most number of films cited (including Gumising Ka Maruja and Gumapang Ka Sa Lusak); Biyaya was the only title cited from Manuel Silos' works, and the only movie in the top ten that was not produced during the Second Golden Age. All of Mike De Leon's full-length features, from Itim to Bayaning Third World, were mentioned. Carlos Vander Tolosa's Giliw Ko (1939) is the oldest title submitted, and Mark Meilly's La Visa Loca (2005) is the newest. Brillante Mendoza, whose independently-produced films only gained notice quite recently, did not figure in the polls.
Among the respondents, 'keating' got 7 from the top ten on his list,while a few came up with 'unique' lists, including 'diabolik' (page 2), totoy bato (page 4), and Jo Atienza (page 10).