There's quality of materials, flange design, and freehub design. There's also the bearings, although many modern hubs can use standard bearings from a variety of manufacturers and grades.

To answer the original question, it depends on the application. Price is almost always a factor, otherwise I'd have tried some Tune hubs with Zipp rims by now. Shimano and Campy hubs are quite dependable, White Industries hubs are light and very purdy, and Novatec and Formula hubs seem to be a great bang for the buck in my experience. My current "lightweight climbing" wheels are on American Classic hubs, which are super light and have been doing fine.