A short contribution to Wikipedia: http://en.wikipedia.org/wiki/Scarborough_Shoal#Claim_by_the_Philippines. Thanks to Jemy Gatdula for explaining these points to me.
The Philippines claim is based on the juridical criteria established by public international law on the lawful methods for the acquisition of sovereignty. Among the criteria (effective occupation, cession, prescription,conquest, and accretion), the Philippines said that the country "exercised both effective occupation and effective jurisdiction over Bajo de Masinloc since its independence." Thus, it claims to have erected flags in some islands and a lighthouse which it reported to the International Maritime Organization. It also asserts that the Philippine and US Naval Forces have used it as impact range and that its Department of Environment and Natural Resources has conducted scientific, topographic and marine studies in the shoal, while Filipino fishermen regularly use it as fishing ground and have always considered it their own.
It said that "The name Bajo de Masinloc (translated as "under Masinloc") itself identifies the shoal as a particular political subdivision of the Philippine Province of Zambales, known as Masinloc." As basis, the Philippines cites the Island of Palmas Case, where the sovereignty of the island was adjudged by the international court in favor of the Netherlands because of its effective jurisdiction and control over the island despite the historic claim of Spain. Thus, the Philippines argues that the historic claim of China over the Scarborough Shoal still needs to be substantiated by a historic title, since a claim by itself is not among the internationally recognized legal basis for acquiring sovereignty over territory.
It also asserts that "there is no indication that the international community has acquiesced to China's so-called historical claim," and that the activity of fishing of private Chinese individuals, claimed to be a "traditional" exercise among these waters, does not constitute a sovereign act of the Chinese State.
Since the legal basis of its claim is based on the international law on acquisition of sovereignty, the Philippine government explains that its Exclusive Economic Zone claim on the waters around Scarborough is different from the sovereignty exercised by the Philippines in the shoal.