How can I tell hotels exist that aren't on the booking web sites?

First of all these websites, backed up by the GDSes as Stephen said, do not have a very good coverage of hotels (yet, it's growing fast). There are still plenty of hotels to aggregate. And for hotels, getting aggregated usually means stricter conditions on their prices (little flexibility and high fee). And the main reason is that most hotels are not owned by large companies but individually owned.

So I would not expect, especially in a remote area, that you find all hotels on these sites. First you should extend your search to hostels (they have private rooms with private bathrooms), b&b, pensions, ... sites like hostels.com or hostelworld.com allow to search for more than hostels. You can try airbnb, couchsurfing and the like.

I would try the tourism board as you did, but that works only if it is touristy. I would bet more on the directories. In most places of the world they are called yellow pages. And there you shall find a list. I can also think of contacting the ferry or airline company that brings you to the tiny island. On their website they might have a list of activities and accommodation. Give also a try to the guidebooks, they are usually done for that purpose. Maps like Google Maps or OpenStreetMap also display accommodation options, even though you should always double check they actually exist.

In the end, if hotels that have a website/can be booked online are still very expensive and you suspect some hotels are not online you can still show up there without a booking. If the area is not big you can cover it fast but if it is an island you should have a backup plan to be able to leave the area before the night not to be stuck there.

I remember getting to a Croatian island off-season and the hostel phone would not ring. I showed up and I could get a room for cheap, but I planned to take the ferry back if I could not find anything reasonable (and it was so dead I really was not sure it'd work). So yeah sometimes you can just give it a try.

I think the answer depends widely on where you are looking. The way I have done this before, is by checking google maps, and doing a simple Google search.

Often a simple google search will reveal hotel web sites, reviews, and simple travel blogs which make mention of hotels not listed on aggregate web sites. Simply search for hotels in <target city>, for example.

Of course the down side is that you often can't book through these resources, but they will tell you that they exist.

I did this once while looking for a hotel in Ajijic, Mexico, and was able to find a suitable hotel, but I had to make the reservation by phone (not always practical if you're booking from abroad).

There are certainly properties that are not listed on a GDS and have no webpage either. Try to find a "City-guide" on the web for each location - and look for a phone directory. They will be in the local phone book. Even if they don't have a website - somebody has probably mentioned them on the internet - somewhere. The phone is still the lowest common denominator in hotel reservations. (skype too)

Expand your keywords for your searches. "hotel" works with most places, but it will miss properties that identify as "lodge, inn, court, motel, stay etc"; not to mention trying the native spelling (non-english).

Some outlier hotels in obscure lands are in locations where they have enough visibility to passing traffic, they generate enough business that they don't need expensive central reservations or a webpage. Its sounds primitive, but this is one of the oldest industries known to man - and just as many rooms were booked without the internet as with it.

Rule of thumb in civilized locales - for every 2 hotels you find on the Online Travel Sites - expect to find at least one that isn't bookable online through aggregators. Usually these are less expensive, budget properties; but not always.

You could always make a reservation to play it safe; and then cancel it within the cancellation period if you find something else you'd prefer once you get there. It's worth asking for a courtesy hold - in which case the room is yours but you don't have a credit card on file; so no penalty for a no-show.

As an out of the box approach - have you considered using google earth/maps to utilize the "street-view" in the city you will be visiting? I would start by looking up and down (and across) the street from the hotel that best represents the caliber of what you would prefer - and see if any of it's "neighbors" are other hotels in the same range. From a aerial view (if you don't have another hotels address to anchor from) - just look for the biggest swimming pool, most lounge chairs and biggest parking lot on a main road. That should be a hotel.

Good luck - let us know how it works.

That's tricky! If you have more money than time, remember that you might spend a whole 2 days looking for better rates to only save $10/night. Sure, I hate over paying. But I could have earned the difference by doing something that makes me money. With that said, if you have more time than money:

The major factor depends on if the hotel is integrated into a major Global Distribution Systems (GDS) like Amadeus, Sabre, etc. or if they are entirely self hosted. A GDS allows real-time booking and updates of room rates, complete with tiered discount codes. How do you know if you're getting the best rate?

Use the aggregator that updates the most and frequently. Kayak's newest deployment hooks directly into many travel agencies direct reservation system, allowing them to compare many different rates in real-time. There are several other sources, but I always find they get to the lowest rates pretty consistently.

If the hotel isn't in a GDS? Unfortunately, they're probably flying by the seat of their pants and their isn't a way to know if you're getting a rate. In my experience, most places like this are completely negotiable, and have a sliding scale depending on how well you speak the local language, and what mood the desk agent is in. The upside is most hotels/B&Bs like this likely aren't in the higher range of the price spectrum, so negotiating may be a moot point when you do the conversion.