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I know I've seen people having Thief and Dark Brotherhood simultaneously. I have bard, mage and companion at the moment. I've not heard of any guilds that prevent joining any others (at least so far).
I can assure you that you can do whatever you want. I did Companions, Dark Brotherhood, Thieves, Mage and Imperial at the same time. The only thing you can't do is join the stormcloaks and the imperials.