This article is from the Triathlon FAQ, by with numerous contributions by James Goddard others.
Both wheel sizes have advantages and disadvantages. 650c wheels
accelerate and climb faster, but they also decelerate faster. 700c
wheels are more comfortable and are more readily available if you need
a tube on the road.
The only people who should be really concerned about wheels sizes are
particularly short or tall people. 650c wheels work much better with
shorter people, especially on triathlon bikes where the geometry
prevents the use of 700c wheels on smaller bikes. Tall riders should
stick to 700c wheels.