I have tried a few different fly boxes but Scientific Anglers System X Fly Boxes have become one of my favorites. Waterproof so your flies are safe. Clear covers so you can easily see the flies in your box and roomy. There are several different models to choose from and the color indicates the type of flies suggested. All of the inserts are interchangeable and there is even a suitcase to hold up to 4 inserts. I like the nymph box. It has a small compartment for indicators and another for split shot. Don't worry about the split shot rollling around, the compartment has an inner lid for them. The clear cases are slightly textured and have slots for lanyards which are nice features. I am buying the suitcase next. I can use it with 4 inserts on my pontoon for river floats or pull two inserts, slap them in a case and I am ready for a wading trip.
Some flyshops have started carrying them and finding them on the web is very easy.
One of the best prices I have found is Cabelas. Although, if you can find them in a local shop you can skip the shipping.
Tight Lines,
Jason