I work in a small dental office and am paid hourly. The schedule is usually full and patients are called and appointments are confirmed. Normally I come to work, clock-in and begin setting up for my first patient. I have recently been told not to clock-in until the first patient arrives for his/her appointment and then the same after lunch (don't clock-in until the patient arrives.) Do I have any recourse in being paid while I am at the office preparing for the patient?

Assuming you are a nonexempt employee (which is nearly a given, since you are paid hourly, unless you are a dentist), if you are "preparing" for patients or otherwise doing work under the direction of the employer, those are hours worked for which you must be paid.
http://www.dol.gov/dol/allcfr/ESA/Title_29/Part_785/29CFR785.13.htm

You can file a claim for unpaid wages with the state Dept. of Labor.

What if my employer was just as happy if I sat in the break room all morning waiting for a patient to show?

Your employer being "happy" and your employer being "legal" are not the same thing. Many things that make people happy are not necessarily legal.