When PFS first started Josh right out made Philosophies not legal for PFS. Since then that has kind been de-emphasized but not really "Officially" made legal or at the least confusing if they are legal. The only philosophies I know are straight out legal with no confusion is Atheism and Pantheism (Additional Resources allow this).
Otherwise, characters who do not receive powers from a divine source may choose to be atheists or to have no deity at all.
I would like to see them added as legal for PFS play, we can start with adding it to the FAQ then a future update of the PFS Guide.
Philosophies are big part of the world of Golarion and it is sad that we can't fully embrace them in PFS play. There are ways around that (Archetypes, traits, prestige classes) or seeing the rules from another certain point of view to get you around it, but when when I want to list my faith I have to pick a deity, a Pantheon, none or atheist. I would rather get the confusion out of it and state straight out that Philosophies are legal.
The rules even allow classes that have to pick deities follow a philosophy:
Clerics who follow a philosophy must select a patron deity among the philosophy’s associated religions (they gain no additional benefits from adherence to a philosophy).
Also from Dragon Empires Gazetteer:
Nothing prevents Tians from being adherents of these philosophies and devoted worshipers of a god; nothing about such an arrangement is strange to them.
Of Course we don't have to allow every Philosophy to be legal, and any Philosophies that does not state associated religions should not be allowed by those that need to pick a Deity, but there are a bunch we should allow.
Here is a list to help Mike and John track them down.
Ones that should be Allowed to be Legal:
Atheism (Laws of Man) – Sources: Inner Sea World Guide, Faiths & Philosophies
Diabolism – Sources: Inner Sea World Guide
The Green Faith – Sources: Inner Sea World Guide, Faiths & Philosophies
Ichimeiyo – Sources: Dragon Empires Gazetteer, Faiths & Philosophies
Pao-Lung – Sources: Dragon Empires Gazetteer
The Prophecies of Kalistrade – Sources: Inner Sea World Guide, Faiths & Philosophies
Sangpotshi, the River of Life – Sources: Dragon Empires Gazetteer, Faiths & Philosophies
Tamashigo – Sources: Dragon Empires Gazetteer
Other Philosophies that are not as explicitly defined as those above but are part of Golarion:
Shamanism (Juju, totemism, ancestor worship, etc.)
We can also open up other rules associated with Philosophies and make it more clear for those who are confused about taking a trait that says you need to be a follower of a Philosophy when then seem to be not allowed.
As an example you can allow the Customized Summon List for Green Faith followers from Wrath of the Righteous: Demon's Heresy.
One of the few Philosophies I would right out say we should not allow is The Whispering Way because it does not work well with PFS.