There are some things about your code that should probably be done another way, in particular using subroutine prototypes is not necessary and usually not desirable. Also, consider using a dispatch table instead of the switch structure using *goto*. Have a look at Implementing Dispatch Tables. I'll leave further comment on this to more experienced monks.

Your code appears incomplete, so I cant really tell what you're doing. Offhand, my solution would be to parse each type of file into a common Perl data structure, then generate the XML from there. I think I would write a separate module to parse each type of input file, so if/when you get a new file type you could just write a new module for it without changing your main program. The configuration file could be used to associate whatever signature you use to identify the file type so you can *require* the appropriate parsing module.

Update: Take a look at module::pluggable