The following method of setting saddle height is the most popular among coaches and riders in the US and Europe. Another article on saddle height gives more recommendations.
First adjust the saddle angle. It should be level or very slightly nose up, no more than 2mm at the nose. Don't forget to lightly grease the seat post and binder bolt. Have a binder bolt wrench ready (usually a 5mm Allen). Put on the shoes you normally ride in.
Mount the bike and sit comfortably, leaning against a wall. Apply a brake with one hand (or just mount the bike on a rollers).
Placing your heels on the pedals, pedal backwards at 30+ rpm, without rocking your pelvis (very important). Adjust seat height so the gap between pedal and heel at bottom dead center is:
Zero to one half cm for recreational riders (under 50 miles/week)
One half to one cm for experienced riders (over 50 miles/week)
One to one and one half cm for endurance cyclists (over 250 miles/week).
Modify these recommendations if your soles are considerably thicker at the cleat than at the heel. It can be difficult to make an accurate measurement without a mirror or friend to do a visual check of your heel and pedal at BDC. This formula has been recently updated to apply to Time and Look style cleats.
Next, ride. It may take a couple of rides to get used to the feel and possibly stretch the hamstrings and Achilles slightly.
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