I use a vernier micrometer. If you aren't familiar, it's a measuring tool that looks kind of like a C-clamp. Mine was an inexpensive version I got from Harbor Freight for something like twenty bucks. I wouldn't use it to measure the O-rings on a solid rocket booster, but it's plenty good for measuring rotors, brake pads, etc. Mine measures up to ten thousandths of an inch, but measuring in the hundredths of an inch is fine for pads.
The small one on the left is the one I have:
They apparently don't sell the small one individually any more. The set of three of them costs $39.99. They also make a digital version (much easier to read) for $35.99.
You can also use a measuring caliper. They look like a ruler with jaws on them. Mine is digital, and will read in millimeters, english fractions, and english decimals. Mine was also a Harbor Freight special, and cost $19.99.
This is my digital caliper:
To measure the pad thickness, I first measure the thickness of the backing plate. Then I measure the thickness of the entire pad (backing plate and the pad material). Usually I'll measure the entire brake pad at four different spots. After I measure the total thickness, I subtract the thickness of the backing material from the total measurement and that's the thickness of the braking material itself. That measurement of just the braking material thickness is what's specified in the service manual. Braking material thickness is 5.8 when brand new, and minimum thickness is .8.
There's nothing wrong with using a ruler. You could even use a nut and a bolt; just screw the bolt through the nut until the nut is resting on the pad material and the screw is touching the backing plate, and then measure the distance on the screw between the nut and the backing plate. I use the micrometer because I have one, and they come in handy for other stuff I do, but they aren't necessary for something this simple.