It's a never ending argument, but here is my opinion.
Air to Air, cheapest and simplest solution, no moving parts. Then you have front mount over top mount. These have there own advantages and disadvantages. Top mounts have shorter flow lengths but suffer more from heat soak and tend to be limited in size. Front mounts have more lag due to size and piping, routing the pipe work and keeping the factory look is also much harder.
So a lot of this decision comes down to use, budget and boost.
Air to water is more complex requiring a pump and heat exchanger, but size for size done correctly can be very effective. The issue here is as some one pointed out before, most heat exchangers for the intercoolers are undersize and suffer heat soak after a short period of time. Some one also mentioned petrol V diesel and time on boost, this is very true. So this also effects the decisions you have.
Their is no easy answer, my own personal frustration is data or the lack of it. Wether it be air to air or air to water few tell you more than what HP they support, when what you need to know is how well they cool and the power gains this gives you.
Marin's TD42 we water to air intercooled returned a 29% gain in torque and 26% gain in KW and retained the factory look. As you can see though the heat exchanger is not small to achieve this. All that was altered was the fuel to match the colder denser air, EGT's are also much lower even with the power increase.
Couple of links with more details.
http://www.patrol4x4.com/forum/showthre ... t=laminova
http://www.outerlimits4x4.com/ftopic164 ... t=laminova
Not forgetting now my little old FJ40 with it's 2F running the same size intercooler as Marin's but in a different configuration. 180rwkw and 560nm of torque
My heat exchanger is in the rear and been petrol much smaller