Generally, I book direct with the airline -- DL, AF, or KL. Last summer VN. I've also bought through Chase rewards points to get the discount. But always careful to confirm the booking codes within the 24 hour cancellation period to be sure I'm booking a SM earning ticket and not an E fare.
But sometimes, expedia comes through -- I booked an MU trip on expedia because the MU site wouldn't provide the fare I found on google flights.
When MU changed the schedule creating a misconnect, expedia contacted me and then arranged for a full refund from MU because a rebook wasn't possible. The expedia agent kept me on the line for about an hour while she dealt with MU cancelling the ticket and setting up the refund. I guess I could have done it myself, but having someone else take care of the details was nice.