Whilst not being an entirely 'natural' solution, I find the best way to cleanse the air after using the toilet is to light a match, this burns away the methane, making it more pleasant for the next person!
Quince fruits, which are ripening on bushes near you right now, impart a wonderful scent to clothes and airing cupboards, in the car or just around the home. They never really rot either - I'm still finding them at the bottom of my wardrobe with no ill effects. Natural sweet scent, and even better, free!
If you are in the states you can get odor eliminators from www.gonzocorp.com. They are made of volcanic minerals that soak up odors like baking soda, but you can re-use them when they stop working so well by hanging them outside in the sun for a few hours. I have one that I've been using in our closet (where we keep our stinky running shoes) for four years now. It's awesome, and doesn't make any smell of its own.