Start iPhone Configuration Utility and from the left menu select "Configuration Profiles"
In the General section of your new profile fill out the Name (MyWebsite app) and identifier (com.mycompany.coolapp). You can add also organization name and description.
Scroll down and select Web Clips section.
In the Label field you can enter the name that will be visible on the home screen.
URL will be the URL of your web site / web app.
Select the icon to be used as a home screen icon. Use at least 114x114 pixel resolution.
If you select "Full screen", the navigation bar and the address bar of Safari will be hidden when you launch your web app, so you can have a real "app".
Click on the "Export" button. You can decide whether to sign your profile (will be visible by the end user when he installs your profile).
Save the .mobileconfig file and upload it to your web server or send to your end users via mail.
When the end user opens the .mobileconfig file on his device, the system will ask him to install the configuration profile. After the installation a home screen icon will be created that points to your web site.