> Ink scape! +10
As an inkscape developer who is bug testing all the time, I have to say that as frustrating it is for me, I can't imagine how frustrating it is for users trying to be productive (not that bug testing isn't being productive). I also hit this issue in GIMP and a handful of other apps.
Having Unity block me on a regular basis is something that makes me consider switching desktop environments... I honestly like Unity for the most part but this is definitely a big source of aggravation for me. If the behavior isn't going to be changed, please make the location of the dock configurable.
Cheers,
Josh