I'd be quite interested to see what people say in reply to this. I'm quite new to MVC style programming, and this in particular is something I've struggled with getting my head around.
FWIW I haven't actually ended up using Zend_Db_Table much recently, but what I've generally ended up doing is having a Model class for each source of data, which might be one table, or could be a combination of tables (using JOIN or whatever), and extending the built in classes, keeping as much of them as possible, but altering any bits which are necessary, to keep the controllers as small as possible - one of the key ideas behind ZF is that you should aim for a 'skinny controller' (ie as little code as possible in the controller - it should basically just get data from the model and pass it to the view (and vice versa if appropriate), but do as little data manipulation as possible).
That probably doesn't help much really... If you give us a better idea of what you're trying to do we might be able to provide more direct guidance!