Question
I have a large old Valley Oak that just had the end of a lower branch removed because it appeared dead and was hanging over a home.

The cut end revealed a dark cavity that sounds like the decay column described on this website. What if anything should I put in this cavity or on the cut end to treat the limb?

Answer
IF I am reading this right you cut the end off a dead branch and now see dead decaying material on the inside of this branch. IF the branch was dead I would cut it back to the trunk that way the wound will heal. When the branch stub is left on the tree the decay fungi will in invade the branch and over time may enter the trunk. Cut the branch almost flush with the trunk and it will heal over without applying anything to the wound. If this is not the situation please ask a follow up question.