References are one of the few aspects of the search process which you can control so take advantage by being prepared.
Ask permission before you list a reference. It is cause for concern if the only information your reference can give is confirmation of employment. Potential employers view it as a red flag if no one can vouch for your skills or work habits.
Verify your information. Be sure the titles, phone numbers, company names, addresses are correct for your references. It is not a good use of your future employer's time to chase down contact information and is a poor reflection of your research ability.
Choose your references wisely. References who can attest primarily to your technical skills may not be the best references to give insight into your management/supervisory ability. You may also want to contact more references than you need and rotate them if you are in a heavy job search. This will keep them from being bombarded with calls, and allow you to offer specific references that can verify specific skills.
Educate your references. Be sure the reference has a copy of your resume. This will help them better prepare a reference to help you secure the position you desire. Discuss the requirements of each job and remind them of your relevant qualifications.
Don't name drop. Candidates will sometimes put the president of the company instead of a peer or direct supervisor thinking that this will impress the company. This won't do anything but frustrate the person conducting the reference, because they won't be able to speak directly of your performance and daily habits. If it's a supervisory position you're applying for you may want to list a subordinate, because they will most likely want to find out about your management style.