Athletic shoes are a huge market, and it stands to reason that some less-than-reputable dealers would try to cash in on it by selling fakes and variants. If you're looking for authentic Nike shoes and merchandise, it's best to play it safe. Here are some web sites and retailers that carry authentic Nikes, including a few reputable dealers with hard-to-find and rare styles.
Niketown.com
Nike's official online shopping site, this is the first place to check for current releases and authentic Nike shoes.
Nike iD - Custom Shoes from Nike
If you're a Nike fan, you're going to love Nike iD - Nike shoes you can customize and personalize by clicking buttons. Select from the available models; choose different materials and colors for different parts of the shoes; specify the swoosh color; and even add your name. When you're done (which could be a while - this tool is too fun to play with!), you can save your design, or order the shoes.
Additional Retailers
If you're not into buying shoes online, here are a few US chains that carry authentic Nike shoes and merchandise.
The above sources are great for finding the latest releases from Nike. But if you're looking for a collectible or hard to find pair of shoes, check out the following sites -- all of which have good reputations and claim to be very serious about only selling authentic merchandise.
In Style Shoes: Specializing in Air Jordans, this site has a huge selection of limited, rare and out of production shoes from around the world. With a mission to educate the consumer, In Style Shoes also has a great deal of information about fakes, including how to spot them.
Pick Your Shoes: With a staff of shoe experts and collectors examing their stock for authenticity, Pick Your Shoes has a good reputation and only sell authentic shoes. Their supply is purchased from authorized Nike resellers, and while many sellers of fakes and variants will claim to be suppliers for this site, don't be fooled - visit their site for the real deal.
And finally, if your Nike-buying needs still haven't been met, you can use this handy tool to locate an authorized Nike retailer near you, or find Nike factory and outlet stores in your area (US).