I believe that what you are describing is how WordPress works out of the box. You will just need to create custom links in your sidebar. Something like example.com/?post_type=your-custom-post-type-slug&theme=taco should query for “all custom posts about the theme named taco”.

Taken from here: http://wordpress.stackexchange.com/questions/17622/custom-post-type-archive-with-dynamic-taxonomy-filtering-is-it-possible