My employer thinks I owe them overpaid commissions from FY06. Because of this dispute I have found another job and plan to give two weeks notice.

Question: Does my employer have the right to withhold my last paycheck, unpaid vacation or unpaid travel expenses. I work out of my home in WA but the company in based in the SE.

They cannot withhold pay for any hours you actually worked. They are at liberty to accept your notice immediately. If they do, it will be up to them whether or not to pay you for the unworked notice time. Some companies do; others don't. If they don't, you may be entitled to unemployment for the two weeks. It can't hurt to apply.

Washington law does not require that you receive any unused vacation time, in the absence of a bona fide contract that says otherwise.

The only state where they are required by law to pay you for travel or business expenses is California, again in the absence of a contract that says otherwise.