If you want to avoid using AppStore as distribution channel and use your own server instead,one possible option is to create so called web-apps instead of native iOS apps. Web-apps are a kind of very sofisticated HTML5 web-pages which has been made to look like native iPad apps.
If you are interested in that, you may want to check out eDocker Tablet Publisher ( http://www.edocker.com )
eDocker also creates a fallback for computer. If someone goes to your web-app´s URL with computer, he/she will see tablet-simulator in his/her computer screen.
eDocker is not free, but if you purchase a license for it, you can use it as much as you like without any additional costs.
If you want to see a sample issue, go to
where you will find a short basic sample ans longer sample with some interactive widget (at seconf half)
Check also this awsome commercial iPad brochure (this is landscape so rotate your device to landscape mode before you start)
You can read those with your iPad´s Safari or you can "install" them by tapping small arrow icon on the left side of your browser´s address bar and choosing Add to Homescreen. Then you will have a customized icon in your homescreen and viewer opens up in fullscreen mode as well. Both samples are working with computer browser too (FireFox, Safari, Chrome, IE9>)
PDF? iBooks has no problems with basic PDF -- I'm assuming your print version does not contain anything iBooks *has* problems with (movies, buttons, Flash...).