As it currently stands, beekeeping is kind of redundant.. It produces mead, sure, but there's easier, faster ways to get my drink on. I'm not sure how useful waxworking is, either. BUT! I have some ideas to make beekeeping more useful, though it might be truer to say I'd like to expand it into a more general "entomology" field.
We've got wild bee colonies, yes, but we've got other insect vermin that just aren't pulling their weight. Imagine if you could gather an ant colony into a container, and give a dwarf a "pet" ant farm. Butterflies could be "farmed" as a beautiful social area.. or for brightly-colored butterfly-wing cloaks for your nobles. Moths could be farmed to produce a non-spider variety of silk (actual silkworms are the larvae of a moth, after all) Wasps or africanized bees could be made into "trap hives" and installed near your entrance to bedevil your foes. How awesome would it be to have a titan or forgotten beast show up, only to be stung to death by 50 hives worth of hornets before your military can even show up? Fireflies could be gathered into glass "lanterns" and used to illuminate dark mines (or just to liven up your dining area) Worms could be released into your farms to improve the soil.
You could even extend the idea into more fantasical realms. Mix in alchemy, and you could get giant dragonflies as mounts. Or ground pixies, stored in tubes as a delicious treat! (mmm pixie sticks..)
EDIT: Just for the record, this whole post is NOT just a long windup to a Pixie Sticks joke. I actually would like to see some expansion of function in the keeping of bees. Thoughts?