If you install Windows SharePoint Services 3.0 on a new server you will find that your Office 2007 (.docx, .xlsx etc) files is not indexed as they should but the old binary document (.doc, .xls etc) format is indexed. This is due to the fact that the Office 2007 IFilters is not installed by your WSS installation.
To resolve this issue you have to download the Microsoft Filter Pack and install it on your server. This will install the actual IFilters which are used for indexing the Office 2007 files.
Then you have to tell the WSS Search Service to index those files, this is a manual registry operation. All details is found in the How to register Microsoft Filter Pack with Windows SharePoint Services 3.0 Knowledge Base article. To describe it short; first you have to tell the gatherer which file extensions to handle by adding all extensions to the registry. Then you have to connect all the extensions to the correct IFilter guid. After all this is done you have to restart the Search Service.
Normally this works fine, but in some cases I recreated the whole index database to get things up and running fast.