Yes, given that collections are really tags, the ability to assign multiple tags is definitely an advantage.
Most devices which properly support folders have an "on-device" file manager of some sort, allowing you to copy or move a file from one folder to another.
I don't know if Calibre allows you to manage your Kindle collections? if so, that may be a useful time-saver.
Collections on the Kindle do work well, I completely agree. It's just that I spent about 2h yesterday assigning fewer than 100 books to the collections where I wanted them on my new Kindle 3; it would be a task of mind-numbing boredom to try it with 5000 books!
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