By bus
The Strong Republic Nautical Highway has made inter-island travel by bus possible. Major islands are connected by Roll On - Roll Off ferries which can carry cars, buses and cargo trucks. An example is the Manila to Boracay route which goes via Batangas, Calapan and Roxas in Mindoro then Caticlan. Philtranco (http://www.philtranco.com...) serves various inter-island routes and has a terminal in Cubao, Quezon City. Needless to say however that these trips can take quite a bit of time and may not be worth the savings if you have only a few days to spend in the Philippines.
Normal provincial buses serving other parts of Luzon also have terminals in various portions of Metro Manila. The Cubao area in Quezon City and the Bonifacio Monument area in Caloocan City is where buses serving the northern portions of Luzon e.g. Baguio, Zambales have their terminals.
The Buendia Ave. cor Taft Ave. intersection in Makati and the area near the Taft Ave. and EDSA intersection in Pasay is where buses from the south e.g. Batangas, Laguna have their terminals.
By Rail
The PNR (http://en.wikipedia.org/w...) rail lines from Tutuban into going as far south as Laguna. A Bicol express line to Naga City is soon to open, while rehabilitation of the northbound rail line is awaiting resumption after corruption allegations stalled them.