Why are some programs in the Ubuntu Software Center not open source?

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http://askubuntu.com – I'm concerned about the amount of proprietary software that seems to be part of Ubuntu now. I've noticed quite a few apps that in the software center are listed as "Licence: proprietary". Obviously there's the partner stuff, like Skype (although that's not good example as it doesn't work in the Software Center) but there seems to be a fair load of other stuff creeping in, too. Is there something I've not understood here? Is it all in partner or is some proprietary stuff in the main Ubuntu repos? Is there a way to filter for FOSS? The open source bit is important to me - I don't just want a (HowTos)