I have the following controlled group situation:

Husband owns 100% of Company A and 50% of Company B. Wife owns 0% of Company A and the other 50% of Company B.

Wife has W-2 comp through Company A and self-employed income through Company B.

For purposes of the deduction, what percentage of the deduction does she get? How do I calculate this figure for her two sets of comp?

There are no specific rules that I am aware of. The amount of the deduction, per entity, depends first and foremost on whether the specific amount can be tracked. If it can, I suggest that is the way to do it. However, in cases where overall compensation limits come into play or where the contribution is determined in a way that doesn't allocate a specific cost to an individual (such as a DB plan) the only thing I have heard the IRS say is "do something reasonable." That, of course, means different things to different people. :-(