Yes, you can -- via custom scope that would include all but unwanted files/folders (Settings | Scopes) and then just choose it in TODO window.
Check these articles for details:
- http://blog.jetbrains.com/webide/2012/10/managing-todo/
- http://confluence.jetbrains.com/display/PhpStorm/Working+with+todo+comments+and+the+todo+tool+window
P.S.
This functionality is available since v6 only.