My wife unknowingly violated the 90-day visa waiver. What should we do?

First you will need a job here State Side that pays sufficient. There is a income requirement. Then you will need to file a 13a. I think it is a 130 form now. Any immigration Office will have them or you can get them on line. And re file. A spouse Visa. 2nd she stayed here illegal. Problem. But find all the old paper work you have. This will make a difference. If or once she is refused. You will need to ask for a hearing. Good Luck There. But if it was a honest mistake. And you were working on it. Before moving. There is a good chance she will be admitted. I would also talk to a Immigration Attorney here. This can take years to do. They like to be slow. So hope for the best the first time around. Also register to vote and talk to your Senator or Congressman. They can put in a good word for you. Some times that helps. Yes you needed to file for a Extension on the 90 day. If you had other paper work going in and they knew you were married at that time. It is probably not a big deal. But will need to be explained to them. They did not have to call or come look for her did they? Then you have a problem. And the time amount you have been married is a big help here. They will know it is more than just a green card deal. A big + there. Have a Attorney write the explanation for the visa Extension failor out for you. One that knows immigration and what form would be required for that.