I don't have an mp3 player/iPod, so I just use Winamp on the computer for playing them. I like to get as complete a discography as possible for my favourite bands/artists, and I'll get the odd loose track by others as and when.
So I have artist folders with album folders inside, and one "Various Artists" folder for the odd tracks. I always run albums through an mp3tag program as well - I use artist, song, album, year, track number and genre tags. And I like to have the album cover in there.
I do like making playlists based on mood or genre, as well.