1. If I choose the backup-function before flashing, do I get a package I can use for an application later?
Does ESIA work on Ubuntu 10.04
Yes it does, I tested it
Are there known issues to use ESIA with windows? Or in other words: Is it better tu use it on linux?
It works better on Linux for several reasons: libusb issues on win, FTDI driver problems with win and the windows USB handling.
I would advise to use Linux native or a VM on Windows.
4. I would like to use ESIA in my SqueezePlug project. Maybe I want to create a Ubuntu-Boot-Stick with ESIA preinstalled to make it very easy to use, would that be possible? If yes, which distribution would you prefere on such a Stick?
Basically you can pick whatever distro you like (Debian/Gentoo/Fedora) and add to it all the stuff you need and create an installation 'application'.