Zazzle has teamed up with Keds to provide a fully custom printed shoe . Every surface of the shoe's fabric can be printed so you can use your creative spirit to make all kinds of designs, patterns and effects. They only have kids and women's shoes right now. If and when they introduce men's shoes, I'll definitely want a pair for myself! They currently cost between $50 and $60, not bad at all.
As blogger Sam Woodfin mentions, it's not 100% clear how the design changes with different sizes. On their t-shirts, the design stays at a fixed size for different shirt sizes. That wouldn't work with shoes. The product images seem to update with the different sizes, so I hope they are accurate. The FAQ seems incomplete; I'm left with questions answered like if they have plans for men's shoes. Still it looks like an exciting announcement and hopefully these questions will be answered in time.
Converse has customized shoes with a number of options and shoe styles. While it's not as fully customizable as you might want, they offer enough options to give you more unique looks than their off the shelf shoes. You can select different sections including the stitch color. Select colors/patterns to make unique combinations in the end. Some parts have more options than others with the fabric pieces having the most options. You can also have text stitched into part of the shoe. I have leather shoes in a customized brown and yellow with the back sitched with "SKETCHEE". Canvas shoes are $60 and leather styles are $75.
Custom Vans' are similar to the Converse customizations, but with fewer color options and with fewer pieces to customize. There are currently only two choices to pick from.
NikeID also gives a few custom color areas and allows you to search their database by color for preselected combos. Depending on the style of shoe, you can print a laser engraved repeating pattern of text or even switch out some fabric parts for leather although not a full leather shoe like converse.
Check to see if your favorite shoes have online customization options by visiting their website. More and more brands are doing it.