Originally Posted by MSPeconomist

You shouldn't charge your clients more in total than your actual cost (unless you bill on the basis of a contract that doesn't allow reimbursement of travel costs). Usually one would explain the calculation, for example with three one way fares, You-A-B-You, where A would pay You to A fare + 1/2 of the A to B fare and B would pay B to You fare + 1/2 of the A to B fare, assuming that each is less than a You to A RT and Your to B RT respectively. [You could also justify some more complicated calculations, but this one seems simple and fair.] In general this is the cost allocation or transfer pricing problem, which has been studied in accounting and other fields.

Where this could become a problem is if either A or B wants the fact that you are working for them to be confidential. In that case, A might be able to guess the identity of B from knowing where you fly after A and similarly for B. In this case, it would be better to just do two separate RTs, even if it's more travel time for you and more cost for each client.