I came up with a way of doing it on Ubuntu. (It works for me but I can take no responsibility). It's explained here. In a nutshell, you need to create a new MIME type, then write a script that works as the app that launches them:
#!/bin/bash
netstat -tln |grep "8902"
# if not found - equals to 1, start it
if [ $? -eq 1 ]
then
ipython notebook / --no-browser --port=8902 &
sleep .5
fi
xdg-open http://localhost:8902/notebooks$1
This always opens the notebook server on port 8902, but first checks whether there is already a server running, and, if so, uses it.
Then you can use ubuntu tweak to select your script as a default application for the MIME type "IPython Notebook" you just created.
Not very elegant, but worth it, in my opinion.