One of the more common questions I am asked is what is the "fastest" wheel depth for carbon wheels.  The simple answer is that there is not one; only a depth that is fastest in the right conditions.  The next question should be "what are the conditions you will be training or racing in."  In most cases the athlete is looking for a wheelset that will give them a distinct performance advantage over their stock alloy wheels that came on their bike.  If they are performance oriented, such as looking to qualify or place in their next event, a carbon wheelset can shave seconds, minutes, even tens of minutes off their time depending on the event.  And this is well worth the investment to a lot of athletes.

Wheel depth yields only aerodynamic advantage and with depth more weight is added to the wheel.  If your course is very hilly depth will decrease performance.  Aerodynamics is mitigated in the low teens speed wise and absent under 15 mph.  In these conditions you want a lightweight climbing wheelset with as little depth as possible.  Consider your course and the speeds you will be riding foremost.  Assuming your event or events don't fall into this category then there are some key questions to ask...

• What is your typical average speed?  If it falls into the low teens you may not be getting much return on investment.  Wind resistance increases with the cube of speed meaning the faster you go the more important aerodynamics become- exponentially important, and the more a wheelset will make a difference.  
• What is your event or typical event course?  Do you gravitate towards more rolling to hilly courses?  Are you more of a climber?  Are there a lot of winds such as a coastal race with cross winds coming off the water?  Do you gravitate more towards flat races where high end speed is a factor?
• What is your event duration?  The short the event, the faster you will go.  Time trialists tend to gravitate towards more depth for this reason as their speeds will be highest.
• Will you be using the wheelset daily; for training and racing?  Certain deep depth wheels are not good all around training wheels as they are heavier, more susceptible to cross winds, and may lack durability.  If you don't want to be penalized in your hilly group ride this is something to consider.

In answering these questions I can usually get them pointed in the right direction.  A good way to think of wheel depth is that the more depth the faster the wheel will be in the right conditions.  Or to put it another way with more depth the more conditional a wheel performs.  Triathletes often opt for a split depth for this reason- deeper in the rear with less depth in the front.  Because of the nature of the tri or aero position a deep depth front wheel can make the bike more twitchy and unstable handling wise, especially in gusting conditions.

There have been some great leaps forward in bicycle wheel technology in the last decade.  Computational Fluid Dynamics, or the ability to test wheels without building prototypes and putting them in the wind tunnel, has aided wheel technology greatly.  At first very few wheel companies could afford, or even have access to this tech as it was very expensive and required a LOT of computational power.  But the early adopters were able to produce wheels that not only cut drag but increased stability.  This was huge as a more stable wheel means less energy is need to control it and it is safer in cross winds.  Prior to this it was a pretty even playing field with a lot a manufacturers touting their wheels as the fastest.  This was backed up by wind tunnel data that showed great results- at a very specific speed and yaw angle.  In other words if the wind was always coming directly at you they were great; from anywhere else not so much.  A wheel that performs well in a variety of real world conditions is a better wheel. 

What if you are a rider that will use a wheelset for training and racing, in a wide variety of conditions, and still wants a performance gain over an alloy wheel?   Generally speaking a depth of 40-50mm is the sweet spot for an all around wheelset, or one that will perform well over the widest variety of conditions.  Less depth and you have a lighter wheel that will climb better but offer less aerodynamic advantage on the flats.  More depth and you have a heavier wheel that will not climb as well but offers more aerodynamic advantage on the flats.  A disc is a very fast wheel aerodynamically in the right conditions.  I do not recommend purchasing a disc unless it is just an added weapon in your arsenal of wheels.

This should give you enough information to make a solid choice on wheel depth but there are a lot of other things to consider, usually foremost is ones budget.  As wheels go up in price you get better durability, better bearings, and more aerodynamic (faster) designs, but you will pay a premium for a relatively small performance gain.  Conversely there are a lot of startup brands producing carbon wheels that do not hold up well or are even dangerous.  The braking surface of a carbon clincher must be very robust and this is common failure point for cheap wheels.  I recommend paying a bit more for an established brand that has some skin in the game and a good warranty.