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 [
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.