There are only five that appear in a day and they appear in random trees. You have to shake the trees to see if a beehive falls out. When the beehive does fall out, a swarm of bees arises and you have to run away, turn around, take out your net, and make sure you swing before they catch you. If they catch you, they fly away and leave a nasty bruise on your face.
In Animal Crossing: New Leaf, the best strategy is to run up a few screens so you no longer see the bees (running down causes them to always be in your view on the horizon). When this happens, the bees actually take a while to "locate you" and come for you. That should be enough time to switch to the net.
I remember in the Gamecube version you had to stand directly behind a tree so you weren't seen (even by you). Then when the beehive fell down, the bees would circle the tree a few times, which would give you enough time to get your net out.
Anyway. What a relief!