I'm jumping in late… so apologies in advance if I am asking something that's already been discussed…
Conrad:
You didn't mention in your original post what type of Steripen you're using? Classic or one of the compact models?
I am pretty sure you'll be fine using the Steripen with wide-mouth bottles like Nalgene Cantene or Platy Big Zips, etc. — as those allow you to stir and fully agitate the water.
For those who suggest narrower mouth bottles like Aquafina — has anyone verified effectiveness with the manufacturer — esp. with the compact models? It's not only whether or not you can fit the light tube through the opening. Treatment requires sufficient stirring to whirl up the baddies close enough to the light tube! Baddies sinking toward the bottom of a long, narrow bottle that's barely stirred will likely survive the zapping — particularly with compact models.
If you have fittings that enable you to treat the water with the bottle upside down — that should be fine — but otherwise, you should check with Steripen — if you haven't already.