How to lightning-proof a structure?

Solution 1:

• Keep regular backups until Notch provides a form of protection against this or a way to disable thunderstorms.
• If you see a thunderstorm get far enough away that the chunks containing your treehouse are unloaded.

EDIT: As of Minecraft 1.6, fire is severely nerfed and will not burn through your buildings like before. Consequently, lightning is also nerfed, and may not be worth worrying about, unless you structure is made of difficult to replace flammable materials, such as certain colours of cloth and leaves.

EDIT 2: Leaves are now replaceable due to the ability to cut them with shears in Minecraft 1.7. As a result, even treehouses no longer need to fear lightening.

Solution 2:

Just sleep through the thunderstorm. Use a bed when one appears.