I have a web app and I want to take photos and then upload them to a server. Can this be done with a webapp?
No, webapp cannot access internal devices. Try PhoneGap to make the gap between your app and the internal devices. But that will compile an application, which need to be distrubuted via the Apple Store.
You'll be able to create 'provisioning profiles' for up to 100 different devices to directly install your apps on, without going through the App Store. The install process isn't as straightforward as calling up a URL or downloading something from the App Store, but at least you can limit distribution to specific people without revealing the existence of the app in the public App Store.
Also see http://stackoverflow.com/questions/37464/iphone-app-minus-app-store
Re. Savageman's answer, we have developed a iPhone web app that taps into the GPS and compass just fine. Not sure why he thinks the hardware is off limits to web apps...