I think you would need to upgrade to Lion where you can search within mail for Mailbox names (including Folders). Double-check by using the search field in your version of Mail to see if it shows a result when you search for a Mail folder.
Even under Lion, the Mail folders don't show under spotlight... only in Mail itself.
Upgrade to Lion is not in the cards for me as I require Rosetta. However, as suggested I have now double-checked the Find functions in Mail and found a curious (to me) anomaly.
Mail (V4.5) has two search functions - the standard one in the Menu Bar that all applications have (within Help) and another that can be placed in the Tool Bar.
A search using the Tool Bar help will generate mail documents that contain the key word(s) but not the Mailbox. However, the mailbox can be located by clicking on "Show In Mailbox".
The Search function, within Help on the Menu Bar, is quite different. The key word(s) not only locate the Mailbox but also have a floating blue arrow pointing to it.
I wonder why the Mail-specific search function wouldn't also be structured to find Mailboxes, if someone has written the code anyway for the Help search function....unless that's what you mean Lion does.
As was mentioned if the word importer is not installed properly that would affect the ability to search by content of word files.
That would be beyond my ability to ascertain....and may be the reason Jon has suggested a system reinstall may be in order.
Also make sure spotlight is not blocked form the folders where the documents are stored via the system preferences.
It isn't. All boxes are checked and the only changes I've made there is in the order of the search items.