This is not going to be an easy problem to solve, but I think it's possible by hosting the web-page in a browser embedded in a .NET application. This Code-Project article might help
Also this article talks a bit about accessing the DOM through a C# application.
Have you got any requirements on language? And can you add a bit more detail about exactly what you're trying to achieve?
EDIT 1: Watij is a web-application testing framework for Java. You can use it to fill in text-boxes, click buttons etc. I think it might fit your needs and, if it doesn't, it's open-source, so you might be able to hack it to work. There is a whole family of Wati* products - Watin for .NET, Watir for Ruby, etc.