Waymate is attempting to do this. As of June 2013, they advertise: “Seamlessly search and compare the time, duration and price of various transport options in one an easy-to-read timeline – ranging from trains and flights to travelling with your own car.”
Also, on the results page, Skyscanner has an option called Non-protected transfers. When enabled, flights combined from different tickets are shown, often a combination of flights by low cost carriers. This is not exactly what you are looking for, but it can be of help: Once when traveling from the Canaries to Germany, I used that option, and then decided to replace one of the legs by a boat trip.
You don’t say if there are any specific areas or countries you are interested in. I doubt there is anything like this that covers most of the world.
However, for the UK, Traveline at least attempts to do this. The interface is dated to say the least, but it’s otherwise quite capable. It covers walking, the train, buses, and coaches (although not air travel, AFAIK).
Deutsche Bahn also claims to cover boat and bus travel, and certainly does for some parts of Europe, although I suspect coverage will vary.
Rome2Rio offers a very rudimentary version of this service, and has recently added prices (no idea how accurate they are), to at least some searches.
Credit:stackoverflow.com‘
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