I am running Thunderbird Mail on Ubuntu 12.10.
How can I un-mark the SPAM notification from known contacts?
If you are talking about the classification that Thunderbird itself does, there's a way. Go to your account settings, there go to "Junk-Filter" (I'm retranslating from German here, so I'm not 100% sure about the wording). There you should find something like "Don't mark messages as junk automatically, if the sender is in one of the following address books". There you can choose one or more address books. If somebody from those address books sends you an e-mail, Thunderbird automatically categorizes it as ham (no spam).
If, on the other hand, you are talking about the markings in the mail subject that some server-side tools like SpamAssassin set ("**SPAM** the original subject of the mail"), it's a different case. In that case you'd have to talk to your mail provider, if and how you can whitelist sender addresses.