I use a standard laptop backpack, which has a padded slide-in pocket for the laptop and a separate pocket into which I pack my flight gear (headset, licenses, charts, whizz-wheel, GPS, stationary). The headset (Lightspeed Zulu) folds into its own rigid case, though, which really helps; I'm not sure this would work with a standard DC or Bose.
My bag is similar to this:
15" JEEP LAPTOP DELL SONY HP BACKPACK/RUCKSACK BAG NEW on eBay (end time 30-Mar-10 21:08:03 BST)
but somewhat smaller. My laptop is a 15", so it's easier to find stuff that fits.