I am using Solaris, but this seems to effect the Linux version as well.

I click on a link that contains an .fdf document. The browser (Mozilla or Firefox) does not know what to do with it. I have set up a mime-type application helper to launch the viewer externally. That works. Solaris version 5 Adobe Reader can view the .fdf file. But what about the plugin? How can I view the .fdf as I do .pdf files using the Adobe browser plugin and do it smoothly like I can with .pdf files?

Firstly you would need to remove any special mime-type handlers that you would have setup in your browser.

Secondly, in the browser type "about:plugins" in the adress bar. This would open a list of all installed plugins. Make sure mozplugger or any other plugin which can handle PDF/FDF mime type is not present. If there is any, you would have to manually find the corresponding file and remove it.

Next, you would need to remove all occurences of the file 'nppdf.so' from $HOME/.mozilla and anywhere under /usr (except from the one existing in the Adobe Reader installation folder). Once this is done, reinstall the plugin by running the script at <reader_install_folder>/Browser/install_browser_plugin.

After the installation is complete, try using the FDF links again. If it still fails, open the /etc/mime.types file and look for the line application/vnd.fdf. Append to this line the word 'fdf' after a tab at the end. So basically the line would look like -
"application/vnd.fdf fdf"
This should fix your problem. Incase you face in issues in between or have anything unclear, just go through the file <reader_install_folder>/Browser/HowTo/ENU/Browser_Plugin_HowTo.txt.