Yesterday, in Laure's call to clean and organize, there were a couple of queries regarding shoes. We culled our idea from a friend with a bigger closet; it's efficient, practical and neat.
We use these plastic drawers from the Container Store we've blogged before. The athletic shoe size holds our heels, flats or sneakers; the sweater size corrals our boots (yes, we fold 'em). Polaroids in the front let us know, at a glance, what's inside. Our shoes stay off the floor and dust free and our closet stays relatively neat. 
These Tweed Drop Front boxes, also from the Container Store, offer a similar, prettier solution without the drawer option.
100 DIY Ideas for the 3-Day Weekend
Danielle's Charming, Classic Walk-Up
Good Food to Share 
The Big Book of Small, Cool Spaces 
Apartment Therapy Presents 
The Eight-Step Home Cure 
White Enamel Flatwa...
How To Cook Fluffy, Tasty Quinoa
Perfect Summer Cocktail Recipe: Honey Bourbon Lemonade
I think one big advantage of using these boxes is that they open from the side, not the top. If you have a bunch of shoeboxes stacked one atop the other, it's going to be a pain to get that pair of shoes on the very bottom. Which makes me wonder, why don't shoe companies start providing boxes that open sideways?
Amen to the sideways comment. All my shoeboxes come tumbling down when I want to wear the pair on the bottom of the stack.
If you have the (mis)fortune of small feet, CD storage racks can be repurposed for shoes. I have two of Ikea Robin CD racks bought of Craigslist for about $10/each (like this: http://www.flickr.com/photos/88878917@N00/124011956/) with more than enough space for all my shoes. I'll try to take a picture of it, because I think it's got its own appeal with the shoes sorted by color. In the winter, the upper cubbies get used for mittens, hats, and scarves since the sandals are all packed up.
I did the whole picture thing with my shoes and boots. And it is really great - the problem, as mentioned in a prior post by spaceagemouse, is opening from the top. Since, I have too many shoe bins, I'm not starting over. This would be an expensive endeavor, so I will suffer silently.
The Container Store sells an underbed shoe storage vinyl zippered thingy with compartments for different shoes. It has a handle to pull it out from under the bed and can hold about 16 pairs of shoes. It's great for storing away out-of-season shoes and can fit under a very low-profile bed.
http://www.containerstore.com/browse/Product.jhtml?CATID=73669&PRODID=64972