drupal 7.12 : multiple taxonomy vocabularies in a single view exposed filter
I recently did the exact same thing for a client. The website is http://www.buyagainbaby.com.

You will notice there are 9 primary categories each with subcategories.  I achieved this by creating 9 different taxonomies. After researching this for weeks, I found this was the best solution. Here is how I did it.

9 taxonomies, each named for the product category you want, Footwear, Trousers, etc, then add as many terms as needed to each vocabulary. Now create one content type for each corresponding category and then assign that vocabulary to that managed fields area. At least this is how I did it.  It was a bit of a chore to get setup, but, bit was worth it. All the search functionality is done with views filters and having it architectured like that lets me do some very complicated things with filters and views.  Let me know if you have questions.  Oh one more thing, keep the content type name the same as the vocabulary name, and that will help tremendously in simplified complicated views to return products, etc.