iTunes is just the same? You put all your music in one folder, you point iTunes to that folder and it picks up all the music in that folder? In fact it's absolutely no different to Winamp!
Winamp doesn't take your files and create a big mess out of them. You just click on the songs you want to play and it loads them up in the playlists and... plays them. I think you're thinking of another application. Winamp was very basic.