
EJVW |

I'm not aware of any spell, prayer, or invocation that lowers opponent's Spell Resistance protection, nor any magical affect that increases one's chance to beat an opponent's Spell Resistance protection, but I do know of two feats that should fill the bill: Spell Penetration and Greater Spell Penetration; each adds to one's chance to break through opponent's Spell Resistance. And they are both core feats.

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Piercing spell metamagic feat:
Piercing Spell (Metamagic)
Your studies have helped you develop methods to overcome spell resistance.
Benefit: When you cast a piercing spell against a target with spell resistance, it treats the spell resistance of the target as 5 lower than its actual SR. A piercing spell uses up a spell slot one level higher than the spell's actual level.
Combined with Spell penetration and greater spell penetration, you can effectively get their SR down by 9 (+4 to your attempt to punch through it, -5 to their SR for that spell).

Fnipernackle |

Yes there is. its a spell called Spellbreaker. Its a 4th level spell with an immediate action casting time and in a 3pp called Eldritch Secrets

Fergie |

I think if you Death Knell a bunch of peons, your caster level will go up. There is also a rune stone that increases the your caster level.
SR is built into the game for a reason. Between spell penetration and greater spell penetration, bypassing SR should not be too much of a problem against most opponents.
Assay Resistance (and the various orb spells) were some of the worst aspects of 3.5 magic in my opinion.