Mobile sites. Not just mini versions of websites. Javascript in Freckle.
mir.aculo.us
mir.aculo.us
http://plugins.jquery.com/project/svg
There's two things at work here:
1. We're a small (2 people) shop; and 2. Our customers use mostly iPhones (more than 80% of mobile browsers that access our application).
For these reasons, we don't have special versions for any other mobile devices now (of course you can still use the desktop version of the app on the device, which works well on Android for example!).
The truth is, supporting mobile devices is hard work. If you want to support other devices than just for example the iPhone you will either need to provide a toned-down version of your app and have the same bad experience for all users; or special-case and provide versions that use the platforms to their full potential.
We choose to make 80% of our mobile users very happy, instead of providing a boring version that doesn't work so well to 100% of them.
Are you using any mobile libraries/frameworks (other than the mentioned iScroll)?
They can only go so far - they give you one standardized experience.
If you want real awesome stuff, you have to hand-code, and for that you want a framework/library that supports hand-written custom code well; thus Prototype.js is the optimal choice here.
You can't just make one version and throw in flexible CSS. That doesn't even work within the iOS platform (between iPhones and iPads).
These are very different, from the point of view of the user. For example, on the iPad it's easy to use multiple fingers at the same time, while on a phone, two or three fingers are the upper limit (and it's really hard to exactly hit a target then).
Next to that, people also have different expectations on various platforms (like buttons being in different locations), etc. etc.
My point is that you can't make one app that works great everywhere. You need to know your audience and provide really great custom-made, hand-optimized solutions. Anything that promises automatic multi-platform compatibility is an exercise in mediocrity.
Who's using Java applications on their desktop? Right, nobody. It just sucks and doesn't work; and that's why platform-specific desktop apps are still alive and well. The same thing is true for mobile web apps.