JQuery Mobile framework works well to style pages with a native look and feel.
You can see the results at http://geonote.org/places/plans for a 'from scratch' look and http://m.geonote.org/places/plans for the JQuery Mobile look.
The first thing to take to heart is the spartan look of mobile web apps. There simply isn't room for multiple crowded top nav and side nav bars or for the data dense (but information poor) layouts of most sites. Take a look at a sample page from AllRecipes (which is a great site) - http://allrecipes.com/Cook/SHORECOOK/Photo.aspx?photoID=602783 - there are nav bars for site section, tabs, breadcrumbs, sub-page navigation and so on. Not to mention a right nav bar with even more links. These are all useful I'm sure, but for a mobile web app you need to start from a blank page and work you way up and consider the information value of each pixel used. (Every pixel is sacred, every pixel is great. If any pixel is wasted, Tufte gets quite irate.) Another way to think of this is to consider each link as an internal advertisement for a page the user doesn't want to visit. There is a name for unwanted links on a page put there for commerical gain and that is 'spam'. Don't let your designs become link spammy.
Next, you will want to have a way to preview your web app on a mobile device. If you have a modern phone then you can use it's browser and point it to your local dev environment, but another way is to use an iframe wrapped in a phone mockup. Here's the one I use http://geonote.org/html/iphone/ There may be better mobile browser emulators but I didn't spend much time looking for something once I had the iframe based "emulator" working.
Building pages for the 'from scratch' look follows the typical web app development path - you can use most any framework you are comfortable with, but be careful with approaches that are 'client heavy'. You'll want the smallest HTML, few images and the least number of resources downloaded for rendering each page.
Many scripting libraries have a way to package only the necessary modules into a single resource - this cuts down on the network time needed to get the page rendered. Personally, I avoid client libraries since they are mostly meant for whiz-bang interactivity and on a mobile device the interaction feels better when it is as direct as possible. Common web app performance advice applies here - caching is your friend, the network is not.
The JQuery Mobile look was the most interesting part of building the UI for this site. I was really looking forward to getting a native look and feel for free. Although the library is currently in Alpha 3 stage it's very usable and I haven't run into any bugs in my limited testing. The JQuery Mobile library changes how you think of browser based pages. Not only does it try to use Ajax for most things it also introduces "compound pages" which results in an ever-growing DOM with 'sub pages' or panels that are shown and hidden during screen navigation. This allows for JQuery to perform the animated transitions between screens that give the hip 'mobile look' which is so captivating.
The downside to using an Ajax approach is the use of local anchors (the part of a URL after the '#' character) for tracking state. While this is certanly a popular and Ajaxy way of doing things it does have it's problems. If you aren't familiar with the details it really mucks up how you work when building pages and causes things to simply not work and breaks the page (requiring the user to manually refresh the page). I still don't have forms working and had to disable the Ajax loading of some pages due to this hash-based URL trickery. You will need to rigorously test all pages and transitions between all pages to ensure that it actually works.
Another downside to using JQuery Mobile is that the user interaction is noticably slower than just a simple HTML and CSS page. It is almost not "interactive", which is not a good thing for client applications. There is a lot of promise though and I haven't even looked at the built-in capabilities of JQuery Mobile for wider screen devices like tablets.