I have spent hours, even days researching whole house fans, and have found them to be one of the most cost-effective energy-saving home improvements one could choose to make.
After sorting through all of information out there, Here's what I'd look for:
Quiet operation - This allows you to run the fan during the coolest hours of the day (the nighttime, while you sleep) and get the maximum cooling effect. Dual speed operation is also nice, because the low speed is in many cases much quieter. Exchanging the air is important, which high speed can do quickly, and low speed can be used over night to cool the thermal mass of the structure down to the core. This way you can use your structure as a 'shield' against the heat the following day, and you can actually get more of a cooling effect with less airflow.
High Efficiency - If you are considering installing a whole house fan, you are most likely trying to save energy by reducing A/C use. So finding the most efficient whole house fan seems only logical. Some manufacturers have begun using ECM (electrically commutated motor) technology, which allows for AMAZING efficiency numbers -- and also extremely low noise levels -- especially on the lower speed settings.
Automatic, Insulated Doors - Unless you like crawling into your attic every season to insulate the hole in your ceiling (or if you live in a mild climate) you'd be better off finding a product that features mechanical insulating doors. Keep in mind that the seal created when closed is as important, if not more important, than the insulation level (R-level) provided. When shopping, ask whether or not the seal is maintained when the unit is off. Without a seal, it does not matter what the R-level is, and the insulation can not do its job.
Good luck in your search, and keep these features in mind when shopping.