I'm going into this knowing that it's probably below the level you're applying for, but it's been OK to state "references available upon request" in your cover letter or resume. In my experience, references are generally checked after the first round of interviews, and that gives you the opportunity to tactfully tell your story.

Then again, I've got a great track record of working for poorly managed companies, so maybe the good ones ask for them up front ;)

Last resort, references are as much about your integrity as they are your technical abilities. There's nobody you've looked at as a mentor, advisor, or trusted peer over the past few years?