I've recently developed a spreadsheet for finding the most efficient freighter designs. You input the range of a typical mission leg, and the spaceport facilities on each side, and then the specifics of your engine design(s) on a separate sheet. Then, you can add components, and the sheet calculates expected crew quarters and armor size. It ends by telling you the cargo tons/BP/hr and colonists/BP/hr on the route in question. You can then try multiple designs, and pick the one that gives you the highest values. It also tells you things like range which may be important for design work.
I think I've gotten all of the bugs worked out, and it shouldn't do silly things like give negative crew quarters. Also, the 'load both ways' value needs some explaining. If set to 1, it applies load times twice, which slightly changes the optimum. Don't put more than one engine type on a design, as it breaks several bits of math.
I built this after one of the players in my multiplayer game designed a freighter (nuclear pulse engines) that did 183 km/s. I decided to see how badly he'd messed up, and ended up finding out that his cargo/BP/hr was about one-fourth of the optimum. I also ended up with a spreadsheet that seems very, very useful, and didn't see that anyone had posted anything similar.
Enjoy.