We get a large amount of data from our clients in pdf files in varying formats [layout-wise], these files are typically report output, and are typically properly annotated [
We use Xpdf in one of our applications. Its a c++ library which is primarily used for pdf rendering, although it does have a text extractor which could be useful for this project.
pdftohtml -xml
although pdftoipe seems more detailed!!
If you're fine with calling something external, you can use ghostscript - look at the ps2ascii script included with the distribution. I'm not sure what you want from a graphical tool - a big button that you push to chose the input and output files? A preview? You might be able to use GSView, depending on what you want.
Have you looked at Aspose? We're using it for an ASP.net app and I've seen some examples of vbscript using it as well. It's not particularly expensive either.
http://www.aspose.com/