Just for grins: it occurs to me that the various plasmid/tonic icons available on the Cult of Rapture Downloads page would make awesome Boy Scout merit badges.
I've played the game through a couple of times now, and it is really hard to go back to nothing once you've had the pleasure of loading yourself up with enhancements (not to mention upgraded weapons and ammo).
The main choice you're given is whether to harvest the Little Sisters for "Adam" (the resource which you trade in for additional enhancements), or rescue them (which gives you less Adam, but doesn't make you feel like a child-murdering sociopath). I haven't tried harvesting some and rescuing others, but rescuing them all gives you a different cutscene at the end than if you harvest them all. Otherwise, it doesn't significantly alter events during gameplay.