File opening doesn't work/ PDFs are opened with GIMP

Midori opens files with GIO, and falls back to xdg-open, exo-open or gnome-open if these are available. All of this relies on freedesktop.org MIME configuration. To tweak this there are multiple options:

1. Use 'Open With' with a graphical file manager
2. Edit ~/.local/share/applications/defaults.list with a text editor
3. Run something like ‘xdg-mime default evince.desktop application/pdf’

xdg-open knows how to handle GNOME, KDE and Xfce. LXDE is unfortunately not supported yet, see https://bugs.freedesktop.org/show_bug.cgi?id=26058