Winamp's Media Library works peachy for me. However, that's dependant on having good tags in your collection. I spent a long ass time taking many many songs I ripped with no tags, and adding tags to them when I started using a media library. But it was well worth it... finding exactly what I want, or just saying "hmm, I'm in the mood for X type music" I can get to it quickly and efficiently. No hunting through folders, and adding songs from various folders into the playlist.
Any duplicate songs will show up next to each other in the library, and you can remove whichever one you want to.