Linking vocabularies to specific content types (page, story, project etc) is great, and what I think is one of the best features of drupal. However, there are definitely elements of this implementation that could be improved. Here are some of my initial usability impressions. Just some initial rapidfire thoughts, as there are some tricky issues which i am yet to fully get my head around. overall i think that drupal sets a very good standard, and i'd like to see it get better...

1) multiple selects are great, but i would find checkboxes far easier to use in forms. i think this interface for joining nodes to terms could be a little more advanced - maybe the admin could control the input type of a vocabularly- select box, radio, checkbox, etc...

2) rather than being static markers, multiple select terms could be able to be filtered - so you could combine two or three terms, and filter the content of the site from this combination, or cruise from page to page with the filter storing your settings, and loading all content based on those settings...

3) logically following on from this, there could be some capacity for assigning specific terms to certain users, this would be particularly useful for sites with magazine focused categories, where there might be individual sub-editors for different sections...

4) different vocabularies have variations in meaning and weight, it would be good to have more options for the way a specific vocabulary interacts with the content/navigation - there could be built in vocabulary types such as Subject , Section , Topic , etc... focusing on being more of a type language, rather than generic labels... just a possibility, and i really have to think it through a bit more coherently - but just thought i'd float a few things out...