Yes, there is a difference. If you want to share files between windows and linux, then you'll need to have Samba running on your linux box (
samba).
To share between linux and linux, then you want to use NFS. NFS is probably integrated into most installations, and it's just a matter of editing config files to share a directory. To access it, you would simply mount the shared directory like any regular device, but specify the filesystem as nfs. You can find the NFS howto
here (in PDF format).