To my mind there are only two countries in the world, Indonesia and the Phillipines, which we can truely describe as insland nations. Japan is not worth being called one.
For touristic travels in these two countries you need user friendly route maps. I have uploaded clickable maps for Indonesia. They are hadly user friendly because the source information is all in Indonesian.
With the Phillipines it is somewhat easier as information is available in English.
1. Manila based routes: https://goo.gl/iiS1jJ
2. Non Cebu/non Manila based routes (1): https://goo.gl/GCZPGh
3. Non Cebu/non Manila based routes (2): https://goo.gl/9f0X2a
4. Cebu based routes (1): https://goo.gl/gxHE2f
5. Cebu based routes (2): https://goo.gl/tJIXZm
6. Cebu based routes (3): https://goo.gl/dMOlQW
Routes and ports are clickable and in many cases further information can be found by clicking on the lines. Alternatvely, you can do so with the legend.
We note that the sheer number of Cebu based routes is indicative of the fact the Cebu is the hub of all places for tourists wishing to spend time in Visayas and areas further south in the Phillipines.
You could start out from metro Manila to places, of course, but I would not advise it primarily because it takes a lot of time, generaly. The only exception may be the trip down to the northern half of Palawan.
Even that can be replaced by air. There are regular daily flights from Manila to Coron and El Nido and once you are there there are now regular fast ferry connections between El Nido and Coron, something like 3.5 hours one way.
The slower Bangka (?) boats take longer, 8 hours, but their operations are stable.
By looking at these route maps and from reading a number of Phyls related blogs it daunts on me that the islands of Samar (bigger Samar) and Leyte are rarely visited by foreigners, much less so by the Japanese.
It may be because of the lingering memory of the largest air/sea battle in history fought between Japan and US/Australia in these waters. I personally think that it is about time we went to these islands in large numbers. That will help local economy of the region.
Ferry companies come and go. I noticed that while collecting information. One of the Lonely Planet's interest was the two international sea routes, Zamboanga (Mindanao)-Sandakan (Northern Borneo, Malaysia) and General Santos (Mindanao)-Manado (Menado) (Northern Surawesi, Indonesia).
I did go to Gen San in July this year to check out on this route. It is closed. With Zamboanga-Sandakan it is my conclusion that this is also closed. These two routes used to be operated by the same company, but it seems to me that they have shrank their operations considerably since.
A few additional and sporadic/unrelated comments are:
1. Dumaguete-Tagbilaran by Ocean Jet is alive. I took that ferry myself in July to catch my flight from Cebu back to Tokyo. Actually, it is Dumaguete-Cebu as I did not need to change boats on the way back.
2. The El Nido-Coron is now OK. The ferry company there, Montenegro, stopped their fast ferry service a few years ago, but they are back in with 3.5 hours one way.
3. Metro Manila-Corregidor trip, one hour one way, is good. It is a flower island littered with legacies of the War. It is very much like Capri minus the furnicular.
4. Puerto Princesa may be too risky at the moment, so are Zamboanga and even General Santos. Davao should be OK, unless you walk into down town area near the river there.
Finally, an extremely useful world map is added here.
This map is actually useful in filling the gaps which my own maps cannot carry.