Taxis

From airports take an airport taxi. You go to the booth, get a ticket and then get the taxi. You pay the taxi driver the agreed fee (usually around 350 peso). In the street, if you grab a taxi it is best to ask if they will take you to the place and then agree by meter. They should have the meter running (by law) - make sure they reset it, something the commonly forget to do! Many will want to charge you a flat (sometimes extortionate) fee though. One con trick that 'meter is broken' - get the next cab! Another is to say they are a hotel car (once you are in) and then charge you five times the rate - agree on meter first. If you agree to a price rather than the meter, get him to keep the meter running anyway as he is required to by law. I usually say 'I'll pay you extra' (50 peso or so) on top of the meter and then they are happy. Typical journey costs about 100 peso. It is normal to lock the doors when you get in, although this is more Filipino habit to be safe, as generally there is no problem. You may encounter beggers/venders at traffic lights, often including children. I suggest you don't give money to them as it encourages them to risk their lives in the road - instead donate to a charity - you'll find many donation boxes in shops. Having said all this though, most taxi drivers are honest and work very hard for just a few dollars a day, so it's good to give a little extra. One other thing - most taxis, especially in Manila, are old and don't have seat belts except in the front. Some drivers are not so good, but generally the heavy traffic means you're pretty safe as you only travel slowly.
Jeepneys

The adventurous tourists like to grab a ride on a Jeepney. The fare is very cheap - something like 8.5 peso, under 10 peso anyway. You simply pass your money to the people in front and they pass your change back. Most tourists prefer an air conditioned cab that takes you directly where you want to go at a very reasonable fare!
Buses

Buses are a great way to get around the Philippines, particularly in Luzon when going to places where flights are not so frequent. Buses are very cheap with fares like 100 to 400 peso depending on where you are heading. They can be a little confusing, so better for the more experienced traveller or people open to adventure. Simply ask around and someone will point you in the direction of the right bus. No need to book, as buses are usually running every 30 minutes or so day and night. To get to some places in Luzon may take all day, but don't worry as many buses are air conditioned (get one of these) and they stop regularly for food and toilet breaks. To find the nearest bus station simply ask you hotel front desk or a taxi driver. Most Filipino's will know where to go as most use public transport to go to the provinces and see their family.
Ferries

Apart from the short trips to different island (like Manila to Corregidor, Bohol to Cebu, Cagayan de Oro to Camiguin, etc.) you are advised to take a flight instead! Flights are very cheap, so why spend a day travelling between Manila and Cebu! In typhoon season, if a typhoon is forecast you are advised to stay put - ferries are not supposed to sail in these conditions anyway. Generally speaking, the ferries frequently used by tourists are in good condition with liferafts and lifejackets.