yEd looks like great software! I would love to use it for my personnal use and in our work place (koumbit.org, a non-profit dedicated to free software and helping other non-profits with technology), but unfortunately, the license of yEd is too restrictive for us. We are worried that the license may not allow us to freely use the software for multiple users and thus threaten the perrenity of our documentation.
Furthermore, as a Debian developper, I would see yEd as a great addition to Debian, and therefore Ubuntu. However, the non-free (as in speech) license doesn't allow yEd to be shipped with other distributions.
I do not see the point in using that special license for this software: users are allowed to download and run the application anyways, why not provide the source code so that contributions from the community could be added to your program?
I also feel it's too bad that you make use of other free software but do not contribute your own back to the community.
Hoping you will make the right choice eventually, which could consist of having a dual license (current license and GPL-2 or similar)...