easier said than done. How do you distribute apps to people outside the app store?
For iOS apps: Most of the time you don't. You could write your app as a mobile web app, but that doesn't cut it for a lot of apps. If you're determined to have a legit iOS app, you're playing Apple's game.
For Android apps: You can distribute on a number of app stores, in addition to or instead of the official Android Market. You can also offer downloads that can be installed manually, although this requires users to change a setting to allow so-called "sideloading" of apps.
Jailbreaking is simple and performed by millions. Support issues aside, if I were selling iOS software I would offer it in the App Store as well as on Cydia.
That said, yes there are alternative app stores available for iOS devices but I would hardly call them "legitimate" since Apple defines that term with respect to their devices. The sad truth is that you have to bypass Apple's restrictions, and continue to do so for each new iOS release, to benefit from an alternate app store like Cydia.
Apple has been treating their developers like crap ever since the app store opened, and the only way to change it is to vote with your wallet (or more accurately in this case, your development time). Otherwise, you are part of the problem.
How does it work? Do you just send ipa files that the user is expected to import into itunes?
People already complain about too much competition on the App store. On the web you're competing with virus' and everything else as well. And people have to figure out where you are.
Having your app on the App store is like having it in some giant big box store. Having it on the web is like having your app somewhere on the planet.