If you have shoes all in similar shades, go with heel height and time of year. Whatever works with the way you think and dress will help you organise your shoes. Get every pair out and decide if they are shoes you really want to keep in your collection. If not, donate them to charity, sell them on eBay, a thrift shop or give them to a friend. It clears out the clutter ... and makes room for more!
Grab a fellow shoe enthusiast and have them help you (offer to do the same for them when they organise their own shoe closet) and get ready to start trying them on. You will try on each pair of shoes you own, preferably with appropriate socks/hose if needed and have your friend take a picture of your feet in the shoes. Position your feet so one is to the side or shows off any special feature like a bow or buckle and one is with your toe pointed to the ground so the top of the shoe can be seen. Make sure it is a fairly close shot so the whole picture is that of the shoes. If the shoes go particularly well with a specific outfit, you can take a picture of that outfit as well.
Are you a box person? Do you like to keep the box the shoes came in, or do you like the uniform look of a clear plastic container? Maybe you prefer shoe bags, or maybe you have your shoes stored in an over-the-door pocket style organiser. You might have so many shoes that you have a combination of these. Whatever you choose, be sure it maximizes your space, protects your shoes (especially the expensive ones) and gives you a clear view. If space or shoe collection size forces you to organise in a way that leaves some out of view behind others, make those the ones you wear the least, or switch out different seasons if that applies.
You now know exactly how many and what type of shoes you own. You should have a photo of each one (print them up as a 3x5 photo) and you should have storage for every pair. Tape the photo of your shoes (and outfits if it applies) to the box they are stored in. If you have them stacked up and behind each other, then use your photos to create a "map" of the shoes on a piece of paper or poster board. The photos will make it very easy to glance at all the organised shoes and find the perfect pair quickly, without disrupting your closet. This will also make it easy to return them to their storage spot when you kick off your shoes at the end of the day.
You can make notes on a piece of paper and tape that next to the picture if you want to recall where you bought them, what you paid, your opinion on that brand or designer, or how comfortable they are (or aren't!) for particular situations. You can also make an extra copy of the shoe picture to put with particular outfits (tape it to the hanger) if your collection of shoes and clothes are both extensive. Another great idea for keeping organised is to have a master shoe list either of what you now own, or what you would like to add to your collection. Then when you are out and a shoe sale strikes, you can be more organised about what you purchase first.
Don't forget to take a photo of each new pair that comes into your collection and organise it into the mix! Also, don't forget to periodically get rid of shoes as they go out of style, wear out or cause too many blisters, so there will be room for new ones in your fabulously organised shoe closet!