I just ignore them all since I have the oh-so useful Sneaky team skill that prevents them from waking up when you walk near them. I haven't noticed any particularly threatening looking sleepers other then a Chandelure in the Breezy Meadow, though.
The more difficult magnagate dungeons have some extremely nasty Pokemon that aren't sleeping all the time, however. The Crokorok in particular are strong enough to two hit KO me, and I was only able to handle them by using a Serperior with Coil to boost my defenses to a massive degree. It also seems like Gothita remain a constant threat no matter what the dungeon's difficulty is, as they're still able to hit harder then most of the evolved Pokemon in the 30s range.