I doubt it had gold or silver like south america.
It gave them access to the China trade, which had many lucrative goods such as spices, sandalwood, silk, porcelain. This was such an important part of the trade system of the Spanish Empire that for centuries they sent Manila Galleons regularly, off the west coast of New Spain or the Viceroyalty of Peru. From the west coast of New Spain (today's Mexico) they would carry the cargo over land to the east coast, to complete the connection back to Spain.
Remember that Spain and Portugal were bound by the Treaty of Tordesillas, so the Spanish had to sail westward and travel through the Americas to get to the Pacific and finally the Philippines. It is also their only direct access -- meaning without going through intermediaries -- to the east Indies, as all other parts were to be the domain of the Portuguese.
Further, as Spain faced increasing competition from their rivals the English, Dutch, French in the Atlantic world, their Pacific route was inaccessible to these rivals until much later.
For a long time in the early period of the European age of exploration, there was significant demand for silver in China. So the Spanish silver mines, sending some of their silver west to Manila, provided a great way to trade with goods desirable in Europe, in essence increasing the value of their trade goods.
http://www.metmuseum.org/toah/hd/mgtr/hd_mgtr.htm
http://repository.library.csuci.edu/bitstream/handle/10139/37/TBManilaGalleons.pdf
Besides what u\itsalrightwithme already said, they served as a way point to the spice in the Molucas archipiélago. The position of the spice islands in the Tordesillas treaty was never fully clarified wo Spain claimed that they were in its sphere and Portugal that it was in theirs. When the Magallanes-Elcano expedition first reached the Philippines in 1520, one of the expedition´s main goals was to find a route to the spice islands and for a time, the Philippines were believed to be part of the spice islands. Later expeditions during the XVI-XVII centuries to the spice islands also used the Philippines as a base.