I'm not sure how important it really is, unless your current layout doesn't work well for you. That is, most things don't really care where you save your documents, code or other files.

Using gnome/fedora quite some time I have the standard Desktop, Documents, Music, etc which sit mostly stagnant due to dropbox.

Some of the interesting others: ~/Dropbox My dropbox folder.

~/prefix where I install various libs and things I'm using. I have my /home on a seperate partition so I can quickly re-install without losing settings. Using ~/prefix saves having to re-build the more obscure dependencies/tools I end up using.

~/projects where I keep checkouts projects I'm working on or using (they get installed from here into ~/prefix). It is also an eclipse workspace folder, for the times when I need eclipse.

~/media a symlink to my other drives (DVD, usb devices, etc) so that when I samba in (rarely) I can easily get to those -- I was too lazy to add shares for them.