Next time you get ready to pack for a trip, head for the produce aisle of your grocery store. Not to buy fruits and vegetables, but to grab a few of those plastic produce bags. You can use them to wrap your shoes so they don't get the rest of your clothes dirty. Any clear plastic bag will do. Your clothes will stay clean, and you'll be able to identify your shoes easily through the clear plastic.
Another idea for shoes is to cut the sleeves off an old sweatshirt and use them to slip your shoes inside so they don't get the rest of your clothes dirty. Or keep those free shower caps you get in hotels and use them as shoe bags. With your shoes in a shower cap, the clothes in your suitcase will stay nice and clean.