Apparently this depends on the manufacturer, but the standing water numbers should be used in most cases. Embraer is telling me that wet numbers can never be used during active rain unless it is a grooved runway and it is light rain or mist. Standing water is 3 mm of water on 25% or more of the runway. Three mm is less than 1/8 of an inch. Most runways can't shed the water fast enough, even if they are grooved, during active rain.
http://www.faa.gov/other_visit/aviat.../SAFO15009.pdf
It really sucks for us Phenom drivers. The landing distance for standing water shoots up to 5,200 feet. You can't make the 60% rule with that at most airports.