without knowing if you're in a Windows or a Mac environment, I can point to both.
- on Windows use Aptana with iPhone plugin to develop iPhone webapps (I guess they remove it, you can use the iPhone plugin with the Eclipse)
- on a Mac, use the XCode.
There are plenty of ways to accomplish the same propose, because I do .NET code and mostly ASP.NET I prefer the Visual Studio environment and with that I use the iUI javascript library that gives me the ability to provide iPhone webapp like, and use the PhoneGap library to get the most of the core feature that, as you can imagine, are not available for webapp.
I also recommend that you register in the Apple Develop Community, the Safari Developer Center (witch includes the WebApps Dev Center), for this, it is free, and you can submit your webapp to Apple through that Developer Center.
Check out some links, specially this one that tells you a lot about the iPhone and WebApps.
If you want to get your hands in a book, I recommend (ISBN 0470251557) Professional iPhone and iPod touch Programming: Building Applications for Mobile Safari (Wrox Professional Guides) it is exactly about developing webapps with iUI.