You can if you [precede the tag in the search with a minus (-)][1].

The following will search across the SOFU for questions tagged <kbd>cmd</kbd> and <kbd>shell</kbd> but **not** <kbd>linux</kbd>.

StackOverflow: http://stackoverflow.com/questions/tagged/cmd+shell+-linux

ServerFault: http://serverfault.com/questions/tagged/cmd+shell+-linux

SuperUser: http://superuser.com/questions/tagged/cmd+shell+-linux


  [1]: http://meta.stackoverflow.com/questions/16462/can-i-do-complex-tag-searches