According to this release from the Mt Baker Climbing Report, the toilets have been flown off the mountain for the season, so bring blue bags:

Mountain Toilets have been flown off Mt. Baker for the remainder of the 2011 season. Climbers are now responsible for collecting and packing out their human waste using Blue Bags or Wag Bags, which can be acquired at the Sedro Woolley or Glacier public service centers.