Pakse is the transport hub of the region, with an airport, bus service and limited boat access off the Mekong. For Champasak and the South, there are more expensive minivans (110,000 kip return to Si Pan Don) from a couple of travel companies ('Pakse Travel' and 'Explore Asia') in Pakse town centre (nearly always packed with bleach blond 20 somethings, don't expect any leg room). From Pakse southern bus station, took songthaew (starting 9am until 11 am; could be very crowded, 20,000 Kip) to Champasak (~2h) or Than bhan khop (2h15), near crossing to Wat Phu. In the latter case, you have about 30min walk to Wat Phu entrance.
Most places in Champasak, including Wat Phou, can be visited as day trips from Pakse.
It seems bus Champasak - Pakse are only available in morning 7am-8am 20,000 Kip, else you need to hitchhike/take taxi.