Available iPhone Web Application JavaScript UI Library/Frameworks
Old question, but still relevant. Sencha (the new name of the company behind ExtJs) just released the mobile app platform Sencha Tounch for iPhone, iPod, iPad and Android:http://www.sencha.com/products/touch/
Blog post that explains the difference between jQTouch and Sencha Touch:http://9-bits.com/post/723711597/jqtouch-and-sencha-touch
Update: John Resig recently announced that the jQuery team is working on a mobile UI library. Looks promising: http://jquerymobile.com/2010/08/announcing-the-jquery-mobile-project/
PhoneGap isn't exactly what you're asking about, but is something you might want to be aware of. It's a wrapper for making iPhone apps using HTML/CSS/JavaScript.
My personal preference is jQTouch. It's a great framework to work with and includes both javascript and CSS assets to make web applications that really give the feel of native applications.
For accessing the lower level functionality of the native device, you can always wrap your HTML files, JS + CSS + jQTouch assets into a native app using something like phonegap, rhomobile or appcelerator, however, this does require a mac to compile and deploy the native application to the appstore.
Certainly most of the things I am looking at are just web applications, so jQTouch does the job nicely. Did a blog post combining my thoughts in my detail on my blog, link below: