With 137 accredited programs out there, selecting schools that interest you can be a very daunting task.  How do you narrow it down?

Degree Awarded

Decide beforehand what degree you want to receive when you finish your schooling.  Some programs do not offer a Master's degree, only certificates and Bachelor's degrees.  The benefit of receiveing a master's is that that is the future of the profession.  The possible drawback of receiving a masters is that you will be required to either complete a master's thesis or a nasty comprehensive exam.  There are also a few schools which do not require a bachelor's degree for admission.  Otherwise, it doesn't really matter which credential you are awarded so long as you pass the certification exams.

Prerequisites

Take a good look at the programs directory and the individual program websites to see if you can reasonably complete their prerequisites by the time you want to apply.  If you simply can't get enough work experience, or if there is just no way you're willing to take that o-chem lab, then it's time to take that school off the list.

Program Reputation

While the US News and World Report rankings are a bit of a popularity contest, they do give an idea of which schools are generally respected as having quality programs.  However, don't let this decide which are your top schools.

Research the schools' first-time pass rates on the PANCE exam.  If you can't find it on the school's website, contact them and ask.  You don't want to go to a program where everyone fails the boards.

Also, if you know any doctors or PAs in the area, ask them their opinions of the program or graduates of the program.

Program Location

As you may have noticed, the Western US is pretty shy on PA programs - most of them are back East.  As you select schools, consider not only how far you want to go from home, but also consider the type of environment you would like to live in - urban, rural, suburban, and so forth.  There are benefits and drawbacks to each including some of the following:

Urban:
Benefits: clinical rotations will all be very close to where you live.  You will see a wide variety of patients and cases in a small area.  These are often the more well-known schools. 
Drawbacks: Housing can be extremely expensive the closer you are to a downtown location.  Not everyone enjoys the fast pace and cramped conditions of downtown living.

Rural:
Benefits:  Housing is usually much cheaper, and there are few distractions from schoolwork. 
Drawbacks:  Some of these programs are extremely remote meaning that travel to and from clinicals will be difficult or impossible.  Some programs require you to find your own housing for clinical rotations that are outside of commuting distance to campus... meaning that you have to move and find your own housing every 4-8 weeks for an entire year.

Suburban: You get the benefits and/or drawbacks of both of the above.

Cost

Tuition at PA schools varies greatly from program to program, ranging from $24k to almost $70k.  The cost of living is also highly dependent on where you go.  Keep in mind as you consider schools how much you are willing to spend on tuition, fees, and general cost of living.

Program Emphasis and Focus

Essentially all programs are focused on extending medical care to rural and underserved populations, but some express this in different ways.  A few schools have an increased interest in international work and encourage that at least one clinical rotation is completed abroad.  Other schools require that a certain number of clinical rotations be completed with an underserved population in the area. 

Each program has its individual mission statement which can be found on their websites.  Read through those and decide whether or not the aim of the program fits with your personal goals in becoming a PA.

Campus Tour/Facilities

Wherever the PA program holds its classes is where you'll be spending all day, every day for an entire year.  If you have the chance, consider touring the facilities and meeting the faculty to see if it is an environment that works well for you.  If you can't tour the schools, that's perfectly fine - most people don't.

How Many?

The number of schools that you choose to apply to is really up to you.  When considering this, think about the strengths and weaknesses of your application.  Someone with a 3.8 GPA and 3500 hours of work experience with additional volunteering probably does not need to apply to as many schools as someone with a 3.0 GPA and 700 hours of work experience.  Most BYU students apply to anywhere from five to fifteen schools.