I honestly don't want to turn this into another "are spells 'weapons'" debate, as I recall there was a huge thread just recently about Inflict Wounds being used for coup-de-graces and I think it got a little ugly, but maybe that's just inevitable...
To me, it seems pretty reasonable that PBS would alter the "to hit" chance of a spell, since it aids in close-quarters ranged attacks - but it doesn't seem right to add damage, since the damage of the spell is caused from magical energies and not necessarily how "hard" you shot it (which is how I think of PBS). Then again, spells with attack rolls can crit, so maybe the extra damage is just representing a more precise hit with the spell...? I guess I'm really just wondering if it is more arbitrary to accept only half the feat or all of it.
(For reference, the question came up from a Melf's Acid Arrow being shot from point blank range. It seems even easier to accept this feat for a spell with the WORD arrow in it than a scorching ray or something similar, but I realize that the mechanics should probably be applied universally.)
EDIT:
Kobold Stew said:
PBS helps with the targeting of a ranged weapon--that little bit of precision which increases the damage.
I missed this before, but this is a good, sucinct way of describing it. I guess if you're willing to accept that the feat helps aim the spell, you should agree that it helps add damage as well.