sudo apt-get install flashplugin-installer
sudo ln -s /usr/lib/mozilla/plugins/flashplugin-alternative.so /usr/lib/mozilla/plugins/libflashplayer.so
sudo apt-get install nspluginwrapper
nspluginwrapper -v -a -n -i
Update: Lewis Goddard has created a script that fixes flash in Midori if the above does not work for you here. Just follow the instructions provided there.
Although this hack works for most people, I still was not able to watch Hulu through Midori. If any has found a workaround, let us know in the comments!
Thanks to GĂ©rald Maruccia for the tip!