My personal paper cut

They will be presented with a file selection dialog box and have no idea that they are supposed to go to /usr/bin, and then wait for Firefox to unfreeze, and then pick one of thousands of similarly named items that have absolutely no connection with what they want to do.

For example, opening a PDF document... how is a normal person supposed to know to select evince? :(

As for the freedesktop.org spec... I actually mis-spoke (typed?) earlier. The spec I mentioned allows programs to declare MIME types (that is, provide a mapping from MIME type to human-readable description). It serves a similar purpose to /etc/mime.types, except that it is more modular (it allows applications to define new MIME types) and it allows for the MIME types to have human-readable descriptions, localized to many different languages.

The spec I should have mentioned is the Desktop Entry spec; this is where applications ship .desktop files (in /usr/share/desktop and other places) that specify (among other things) which MIME types an application may handle. It is similar in purpose to the mailcap mechanism, but again it is more modular and allows internationalization, as well as desktop integration (e.g., application menu entries are derived from the .desktop files).

So, Firefox should be reading these .desktop files and offering the user's default handler for a file, along with a selection of other applications that declare that they handle the MIME type. On my system:

$ grep application/pdf /usr/share/applications/mimeinfo.cache
application/pdf=evince.desktop;gimp.desktop;