Updating with my experiences from this month's trip to Laos: we flew BKK-CEI on Thai Airways and then took a prepaid taxi from there to the Houei Xay border. This cost THB 1500 and was extremely easy to organize at the airport. It took a little over an hour to get to the border. There's no bridge over the Mekong there, just a bunch of fairly rickety boats, one of which took the two of us across right away. The visa process on the other side of the river was quite simple--we paid USD 36 apiece, which I believe was a little extra because it was a Sunday. Whatever! We had no idea where our hotel was in Houei Xay, which quickly became a non-issue because the whole town is about three blocks long.
On our way out, we left from Pakse and drove to Ubon Ratchathani airport. This time we had thought ahead to get our tour company to organize a car--well, two cars, a Lao car from Pakse to the border and then a Thai car from the border to the airport. Total travel time including the border crossing was a bit over two hours. We had built in a lot of padding in case it took longer, so we ended up sitting at the (very basic) Ubon airport for about 3.5 hours. Pretty boring, but better than missing the flight.