They have some pretty cool webapps also: http://www.apple.com/webapps/ on which you can get listed pretty easily.

I'd say webapps are still the way to go unless you need access to some hardware that isn't exposed to the browser.

Not just Javascript, but Mobile Safari has goodies to let you style web forms with iPhone UI appearance, such as sliders for toggling things on and off.

So given that there is already a huge trend away from standalone apps and towards browser apps, Apple is actually supporting that trend by making Mobile Safari apps look attractive and work well on an iPhone.

Have you tried browsing without js? Doing without flash is considerably easier. There aren't that many apps written in js either.