I know this is an old post, but just wanted to give an answer to any that might find this thread.
I am the owner of the open-source Embroidermodder application, it is an embroidery software that can read a wide variety of formats. Currently we can save to the majority of popular home embroidery formats.
We will be releasing an alpha version 2 of Embroidermodder soon. We use Qt as the front-end and cross-platform C on the back-end, so we can run on Windows, Linux/Unix, Mac, and a theoretically on many others but are currently untested.
Take a look and see if it does what you want, otherwise we are an active project and should be able to focus on any particular issues that you might have.
Project home: http://embroidermodder.sourceforge.net/
Binary files: http://sourceforge.net/projects/embroidermodder/files/
Current cross-platform source: https://github.com/Embroidermodder/Embroidermodder