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).