I found the corresponding bug upstream
http://bugzilla.xfce.org/show_bug.cgi?id=6422

Apparently, exo-open simply calls Thunar to open files, and Thunar is
broken. My workaround so far is to keep a copy of Thunar1.0.1 in ~/bin
around even though I'm using the PPA (for the improved sidebar). I then
wrote a small wrapper shell script ~/bin/exo-open which replicates part
of the functionality of exo-open (calls Thunar1.0.1 for files, and mail
client / web browser for links). That's good enough for me right now.

Thank you, Charlie and Lionel, for your support.

** Bug watch added: Xfce Bugzilla #6422
   http://bugzilla.xfce.org/show_bug.cgi?id=6422

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exo-open is broken (doesn't remember the preferred applications)
https://bugs.launchpad.net/bugs/584343
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