Up until recently I never used the tags in Calibre and had no idea that they added the books into collections.
I basically use the tags so that I can identify which books I have read and which book sI have copied to the reader. This way if I ever need to add all the books back again I can quickly sort on the unread books or if I haven't yet copied a book to the reader I can find this by checking which don't have the copied tag...
I was quite surprised when I checked the collections one day to suddenly find a few extras that I never expected to see
Now that I know about it I have considered using them.
One thing that would be great (but I doubt possible) would be to have a filter on the reader itself so you could find books that were only in multiple categories eg a book that was tagged comedy AND Sci-Fi - it would help if you were after a specific type of book...