The Site Collection is the boundary for many things (eg. permissions, content types, rollup, etc) therefore careful planning is needed.
That siad, it is possible to re-parent sites...
Themes are scoped to current site (web).
Maybe site columns will help...
There are a great many considerations to the IA of a WSS deployment, if you can post more info I'm sure the community will be able to help steer you ;)
Matt GrovesManaging Consultant (Information Worker Solutions) - Trinity Expert Systems Ltd [
www.tesl.com]
Blog:
www.mattgrovesblog.com