Look also at http://www.bikesatwork.com
, as they have a good treatease on what makes a good trailer (from their point of view). A lot comes from personal preferences:
The BOB is very narrow. Two-children trailers are typically 32"-33" wide. If you can, try to make is 24-25" wide, which is about the width of a single-child trailer or of the Burley Nomad. Less wind resistance and it's also not wider than you are.
1 or 2 wheels
Single wheel is easier off road. If you design a hitch like the BOB's, the trailer wheel tracks almost in line with others, which is great for tight off-road trails.
Also, single wheel, even à la trail-a-bike tracks perfectly on roads where you don't turn that tightly.
2-wheel trailer is easier to load, easier in stop and go circumstances, as the trailer remains upright. Because wheels are almost in the centre, there is less weight on the rear wheel. It doesn't lean in curves, however, which means that very fast tight turns are out of the question.
A 2-wheel trailer isn't much wider than you are, but while you can squeeze your arms in a tight spot, you can't squeeze the trailer as easily.
If you like to ride exactly on the white line, you need a bit wider of a road. That might make you less comfortable in heavy-traffic situations.
I like the ramblings made on the "Bikes at Work" website. That being said, for 50-100 lb max, my preferences go either for a left chainstay and seatstay hitch for a 2-wheel trailer (actually I prefer one through the quick release because I don't hit my feet on it), or for a rear-rack-based hitch (à la Burley Piccolo) for a single-wheel trailer.
From personal experience, I can say that the hitch of the Addams Trail-a-Bike wiggles after 1200-1500 km, while the hitch of the Burley Piccolo doesn't. I suspect the old hitch of the Alleycat trailercycle was steadier (it was using the seatpost but had a larger fixation).
For off-road riding, the larger the wheel, the more easily it will go over bumps, potholes and the like. That being said, especially for a 2-wheel trailer, there isn't too much weight on each wheel, so I don't think using 16" or 20" wheels really makes a difference in terms of drag. Many recumbrent bikes use a 20" front wheel and nobody complains about the drag...
If you plan to tour, however, get either 20" (fairly easy to find) or the same size as your bike's wheels (less spares to carry around).
Another even more important point: get wheels with good bearings, which might mean one of the better frames with fixations on both sides, so you can use regular front wheels.
Alas, one problem with larger wheels is that you either need to "trick" your frame, or you end up with a much higher... and unstable cargo.
That being said, the trickiest problem is the hitch. One way to get around it would be to look at garage sales and find a used low-mileage trailer and work from that.