Read my earlier post on this subject http://www.sharepointu.com/forums/t/530.aspx
Basically it involves creating a "My Network Place" to each of the document libraries (the source library on your SPS2003 server and the target library on your MOSS2007 server). Once you have them setup you can simply drag-and-drop the files (or copy-paste) from the 2003 library to the 2007 library and bring over whatever folder/subfolder structure intact.
You can alos do this with the explorer view, but in my experience it's a bit kludgy and can time out on occasion. We're currently using the My Network Place option for migrating multiple thousands of docs from an old intranet SPS2003 box to a new WSS 3.0 box and have yet to experience any problems with this method.
Hope this helps,
- Dink