A cart and a small boat have the same cost (100 gp.) A wagon is bigger than a cart and thus costs double. We can suppose that a wagon has about double the capacity of a wagon -- so doubling the size of a wooden land transport doubles the cost. Rafts can be considered a little smaller than a cart, but they aren't as difficult to build as either a wheeled vehicle or a rowboat/canoe, so they cost much less (40 gp.)
Doubling the length of a galley triples the cost; doubling the length of a sailed ship quadruples the cost. This is because larger merchant vessels are usually designed to carry a lot more than double the cargo, so they are doubled in all three dimensions instead of just two. A small galley costs twice as much as a small merchant ship, since it must be built with oar ports and stations, in addition to a mast.
A small merchant ship can potentially carry a couple hundred people in cramped conditions, while a small rowboat might carry four in similar conditions. So, let's relate the cost of a small merchant ship to a boat based on capacity: it costs 50 times as much as a boat, or 5000 gp.* This gives us the cost of the other three ships as well.
* If you were using ship prices to guesstimate housing prices, you could compare the desired number of occupants to that of a galley. A two-story building for a small household (25-50 people) would be about 1/4 the cost of a small galley.
Animal transportation (horses) seems to be based more on speed than on carrying capacity; the light riding horse costs more than the draft horse. On the other hand, warhorses are priced according to capacity and value in combat, with the heavy warhorse costing twice as much as a medium warhorse. Since there are only two non-warhorses given, perhaps we can assume 30 gp for a (medium) draft horse is the standard and use multipliers as for equipment:
- x 1.5 for additional feature (faster, higher capacity)
- x 3 for war-trained mounts