I presently have 5513 songs which amounts to 45GB. Recently acquired a hi-fi and don't want to compromise on sound quality, so I'm in the process of replacing my MP3s, many of which I acquired via dubious means when I was younger and poorer, with Apple Lossless rips from the original CDs. It's gonna take a while, though.
As for organising, I have iTunes set to copy any music I add to my library folder. So long as your music is decently tagged, I don't think it matters how disorganised the file structure is, although in reality iTunes does a reasonable job. Currently, when I can be bothered, I'm going through my collection, tagging it correctly and finding the album art. The automated tools like MusicBrainz are pretty good for released albums/singles, but understandly don't quite cut it for more obscure stuff like early EPs, etc.
The duplicates problem annoys me. For example, I have pretty much the entire R.E.M. discography, which means I have some tracks up to four times. I don't want to waste the space storing three extra copies, but I don't want to delete them and ruin the albums. What's needed is a way to abstract the tagging info from the actual music data, so you could have one file appearing in multiple albums.