Step 1: Choose your natural odor absorber
The goal here is to make something that absorbs smells, not just pushes them out -- much like the box of baking soda you keep in your fridge. A lot of products do this, but they all have fatal flaws that make them less than ideal in this scenario: baking soda or kitty litter would be a clean-up disaster; laundry sheets smell like godawful synthetic flowers; vinegar is great... but driving with an open glass of vinegar in your car is an inconceivably horrible idea.
Instead, you want something that's not going to break down, and that either gives off no odor at all, or something that you'll find pleasant.
Unscented: Activated charcoal or aluminum silicates (called zeolites, shown above) will get the job done and don't give off a scent.
Scented: Wood chips are a fine option and give your car that cozy-cabin lumbersexual vibe. We went with whole coffee beans -- they work great and make your morning commute extra zingy. The best part is that these are all-natural materials, even if they can be mass produced. No chemical smells.