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Papers gives you the ability to group your articles into different "collections," which are essentially the same as playlists in iTunes. I find it very useful to set up collections for each class and sub-collections for each week of assigned reading. It almost makes 30 hours of journal reading per week fun!
Papers is free for 30 days and $25 with a student rebate.
I hate iTunes, so very much.
What program do you use and what about it do you like better? (Besides that it's not Apple.)