5 on 5.5 means five lugs on a 5.5" diameter pattern. This pattern is common to Early Jeeps (prior to the Wrangler), Broncos and 1/2 ton Fords, Scouts, and Samurais, among others. It is not common on trailers, but is used sometimes to match the pattern of the tow vehicle, in order to reduce the number of spares required, or to make better use of the spares being carried.
5 on 4.5 is a common pattern on trailers, and it is used on some vehicles, though I'm not sure exactly which ones. I think this is the pattern used on the Wrangler, but I'm not sure.
There are also some 4 lug trailer hubs, primarily found on lightweight "kit" trailers such as those found at Harbor Freight. I'm not sure what the lug diameter of this pattern is, though I think it's 4". I would expect this pattern to be shared only with some compact cars, though I have never checked into this.
Another pattern sometimes seen is the 6 on 5.5", which is common to 1/2 ton Chevy 4x4 vehicles and some Import trucks (Toyota, Nissan, and Isuzu, I believe).
Beyond that, there are some 8 lug patterns as well, but they are primarily for heavy duty applications.
As you can see, there are several hub patterns available for trailers, but unless you're trying to match the pattern of the tow vehicle, it's probably best to stick with the 5 on 4.5" because of its frequent use. Spares for tires/wheels and hubs can be found in many places, where the spares for the other patterns may not be found easily. The only reason I can think of to change the hub pattern on a trailer would be to match the tow vehicle, and then only for a couple of reasons. One reason would be that you could match the wheels of the trailer to the tow vehicle for a custom look. The other reason would be because the spare tire(s) could fit either the tow vehicle or the trailer, which could be desirable when travelling in the back country.