Well after searching the forum for a while, I thought that having a thread specifically for discussing the best fan controller for our application might be in order..
It seems as if the following fan controller may work very well, as they have thermal sensors, and can display up to four fan speed and temp, along with some temp warnings.
CoolerMaster Aerogate II or Aerogate III
Aerocool Gatewatch.
There are plenty of other ones, and I think it would be great if everyone using one would put in their recommandation.
Finding one that controls the fan's rpm according to the temp may be a good idea also.
Let's start the hunt!!