When I use snapping I tend to put the origin on top left.
'Cause it's size and position that are really snapped, not bounding box... (maybe it should be the other way around? I wonder)
Anyway if you have a 32x32 grid and you put side by side a 32x32 and a 64x64 sprite, they will align their center, so of course you'll have 16px margin around the small one and border won't be aligned.
Put the origin at top-left and your done (:
Anyway, sometimes you need the origin to be centered for rotation thingy, so yeah maybe bouding box snapping could be a neat option. I leave the reflexion to you and to @Ashley maybe (:Yann2012-01-15 19:16:51