Most of the islands in western Visayas are easily reached by direct flights from Manila, and some from Cebu, via Cebu Pacific (www.cebupacificair.com) and Philippine Airlines (www.philippineairlines.com). Caticlan Airport, the gateway to Boracay is likely the busiest airport. Both Busuanga and El Nido are accessible via direct flights from Caticlan on Air Juan (www.airjuan.com) and Air Swift (www.air-swift.com) respectively.
Nearby Kalibo receives direct international flights from a number of cities in China and Southeast Asia; try Cebu Pacific, Philippine Airlines, Air Asia (www.airasia.com) and Silk Air (www.silkair.com). It also has domestic flights. Elsewhere on Panay, Iloilo is a convenient airport with a few international flights, as well as direct flights to Cagayan de Oro on the northern coast of Mindanao.
Negros has two fairly small airports in Bacolod and more importantly, in Dumaguete, which is the gateway to the tourist attractions of the southern part of the island.
The island of Siquijor is linked with short flights to Cebu on Air Juan. And Romblon province is accessible on Cebu Pacific flights from Manila to Tugdan airport on Tablas.
There are so many ports and so many routes in the region that, well, there's a reason the Philippines has a 'nautical highway' system. Companies come and go, routes change, get suspended and then resume and schedules seem to change with the winds. That being said, a few major routes are pretty much always in service.
2GO Travel covers some of the major routes, including connections to Batangas (the gateway to Manila) from Iloilo, Roxas (Panay) and Tablas Island (Romblon).
Roxas is also the departure point for boats to several ports in Masbate. And Roxas, Mindoro is reachable by boat from Odiongan, Tablas Island (Romblon).
Oceanjet has fast ferries from Dumaguete and Siquijor to Tagbilaran, Bohol. And the island of Cebu, just across a narrow strait from Negros is easily reached via several ports, including Dumaguete and San Carlos, further north.
You can reach Dapitan, northern Mindanao from Dumaguete on Aleson Shipping Lines.