I found a pretty thorough article on this subject that I thought I'd share with everyone. Please feel free to add your own tips or links to similar articles that could be of use.
Winter Storage for Motorcycles by Adam GlassThe article above covers the following topics:
1. Storage & Required Tools
2. Filling the Tank & Stabilizing the Gas
3. Changing the Oil
4. Using a Stand
5. Spraying Fogging Oil in Cylinder(s)
6. Covering Intake/Exhaust
7. Final Fuel System Checks
8. Removing and Charging the Battery
9. Washing, Drying, and Waxing
10. Protecting the Bike's Exposed Metal
11. Locking it Up
12. Covering It
13. Things to Do Over the Winter
14. Taking the Bike Out of Storage