There is a plethora of information on the web about how to design web applications but, just to get started, here are a few points to help you on the way to designing a great user experience.
Plan before developing. Start with the user flow and understand how the application should fit together and interact.
Focus on what you want the user to be able to do.
Ensure buttons and menus are easy to find and use.
Avoid clutter.
Design for repeat use. A web site may be visited once or twice but a web application could be used continually throughout the day.
Provide Feedback. Let users know when their request is being processed or has finished processing.
Use transition to lead users into a different interface.
Keep a consistent interface throughout the entire application.