Can I have the 500,000 exclusion on one house with wife and a single $250,000 exclusion on another home after she died and sold both homes in the same year?

If you find something that says you are eligible for a $750,000 exclusion, you are good.  But without finding that something, I think your client is out of luck.

Any chance you are in a community property state? You may have a step up bases on the entirety of the second house, If not comm. prop state you still may have a partial step up bases.

I don't know the details of your client, but it seems questionable if BOTH residences qualify as their "Principal" Residence that would qualify for the full exclusion, unless there was also "Nonqualified Use". It could happen, but be sure to check your facts before even considering such a thing.  Look up the rules for "Nonqualified Use".

The second house was within two years.  Did the husband move out for a qualifying reason that would allow a second home to qualify for the exclusion less than two year after the other home was sold?

As was mentioned, don't forget to consider the "step up" in Basis for the second home becauseof the death.

My understanding is one exclusion every two years.  And only for the primary residence.  

Did they sell the first home while she was alive and bought the second for their primary?  Did he sell it because of her death?  

It sounds like your best bet on the second home is the step-up as @jeffmcpa2010  suggested as long as the deceased was also an owner of that property.  Even in a non-community property state you can get the step up on half.

See this: https://www.irs.gov/publications/p523

partial exclusion...unforeseeable event

"you may still qualify for a partial exclusion of gain. You can meet the requirements for a partial exclusion if the main reason for your home sale was a change in workplace location, a health issue, or an unforeseeable event."

"Unforeseeable Events

You meet the standard requirements if any of the following events occurred during the time you owned and lived in the home you sold.

It's best not to keep starting fresh topics for this same subject. But in both topics, now, you've been asked: is your taxpayer in a Community property or Common Law property State?

No one can answer how step up basis applies, without knowing where these people live.

It would likely be helpful to you to put this into google:

community property step up basis

And now you can read what to do.