I know InDesign and QuarkExpress can do this. But does anyone know something else? Some open source tool would be nice. But any hint is appreciated.
Anthon is correct but he doesn't really explain why he is correct which is what the real question is about:
EPUB 3 supports video in ebooks. Quark and InDesign are two commercial top notch desktop publishing software that have both (finally) integrated EPUB exporting into their software because of the rise of popularity in ebooks. However, this is an extension of their original application which is simply meant for static layouts. A good way of thinking about an ebook is to think of it as a simple locally stored website. It can do most of the things that a website can do, just like you see websites with videos in them, so can an ebook have them. And like a website, ebooks are written in HTML (XHTML if you want to be specific) CSS, Java, with support for images, videos, etc. All HTML CSS and JS are at the end of the day is plain text with tags. You can learn more about these languages at places like codeacademy. Thus, all Indesign and Quark do is automate the writing of this code by trying to assume what you meant from the static layout of your earlier design before export.
If you get notepad+ (free) and have the ability to unzip and zip an epub into its constituent parts then you can literally write all the code out by following the EPUB 3 specifications. Your best bet however, is probably something like pressbooks http://pressbooks.com/, which allow you to lay out the design of your ebook much like you would in Indesign and Quark and which you can export into an epub for very little money - esp. when compared with Adobe products.
Hope this makes sense, I tried to unpack a bunch in a little bit of space based on what I assumed was your knowledge level.