Lots of applications do FS searching and keep a database of files that you can sort in any way you feel like, so the FS directory structure is less relevent.
Amarok is probably the best example of this. You can go in and edit songs metadata indivdually. Personally I use GMPC frontend for MPD, the music player daemon. It's just a sort of background service that just plays music.
For file system management a nice application to check out is 'midnight commander' or 'mc' from the command line. It's a dual-plain style file manager that runs from a terminal, so called 'orthodox' style manager. It's nice because it has a shell built into it so you can type out commands while doing operations in a fairly seemless way. It's very fast, very efficient in terms of user interface. The fastest way to manage files besides scripting. This is the fastest way to manually manage a lot of different files and a lot of different directories.
For automatic management of music files and mass id3 tagging I don't have any sort of recommendation. I know that some exist, but I never used them.
When looking for applications to try out a nice place to look for them is freshmeat.net It's a online website that houses a database of most known Linux software. You can pretty much always find what your looking for, although you need to pay attention to the last time something was updated. Lots of projects haven't had any usefull releases in a long time.