Here's how I measure hubs.

You need a set of parallel ends for this to work properly.  I use the ends of my Park TS-3 stand.

1)  Measure the total hub width.  This is referred to as the O.L.D. (Over Locknut Distance).

2) Measure the distance from end to flange.  I normally work with the left flange since I can brace the rest of the calipers against the stand for accuracy.  This picture is for demonstration purposes.

3) Measure the width of the flange.  I prefer to so this at a spoke hole.  Be sure to angle the calipers so they are parallel to the flange.  Some flanges angle towards the rim.

4) With those measurements, calculate.  Subtract end to flange measurement from half the O.L.D.  Also subtract half the flange width to this number.  The result is an accurate center of hub to center of flange measurement.

5) For the P.C.D. (Pitch Circle Diameter), I have another caliper that has what are called centering gauges on them.  I had to grind the sides of my centering gauges to clear the cassette carrier.  Remember that PCD is not to be confused with the overall diameter of the flange.  You need to measure the diameter of the circle created by the spoke holes in the flange.

6) Last, you need to measure the diameter of the spoke holes.  This is easily done with a standard set of calipers so I didn't include a pic.

With these measurements you can accurately enter them into any spoke calculator.  I recommend the spocalc.exe by Damon Rinard.  It's online, can be downloaded, and free.