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I'm a bit confused about Spell Resistance. If I cast Flames of the Faithful on a weapon (a bow in my case), does SR apply to the arrows shot from that bow (or in the case of a melee weapon)?
The spell says under Spell Resistance: yes (object, harmless)
What exactly does that mean? Since it can only be cast upon the Inquisitor's own weapon, in what circumstance would SR apply (or a saving throw, for that matter)?
The SR line on that spell simply means that if the holder of the weapon you are casting it on has spell resistance it might not work (the creature has to voluntarily lower its SR or you have to make a caster level check as normal).
creatures struck by the weapon get no spell resistance to avoid the affects of the spell.
When dealing with Spell Resistance the terms (object) and (harmless) mean the same thing they do when dealing with saving throws. see pages 216-217 of the core rulebook.
I get that with this spell it is unlikely to ever come up due to other limitations written into the spell... but I can still see a possible scenario where the inquisitor has an intelligent magic weapon that doesn't want to have the spell cast on it and such a weapon could resist the spell via a saving throw (and spell resistance as well if such is possessed).