When you leave the cord pulsing, you are giving your child his or her first autologous stem cell transplant, not to mention, 1/3rd more blood that actually belongs to the baby, and many, many months worth of iron supply.
Even though a major chunk of the cord blood transfer happens over the first 2-3 minutes, the best option would be to let the cord completely stop pulsing before clamping.
Here is a wonderful TEDx talk on the benefits of optimal cord clamping: http://www.youtube.com/watch?v=Cw53X98EvLQ&feature=player_embedded
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