For starters, TCP/IP works equally well in both operating systems. Other protocols of interest include:
Yes.
Tcp/ip
The network layer protocol is Trivial File Transfer Protocol (TFTP)
No you can use multiple protocols.
NDIS
protocols used for network device.
H.323 gateway. network + page 561
These are called protocols - a standard set of rules for common communications across networks.
DECnet from Digital Equipment Corporation is a suite of protocols which may be used on large networks that integrate mainframe and minicomputer systems. It is a routable protocol. DNA - Digital Network Architecture.
The Windows server OS has the ability to establish and manage a domain network. A Windows client on the other hand can only join such a network but not control it.
Routed protocols are the best paths in a network along which to send network traffic.
I'm not sure what you mean by "directly." Data can be transferred between the two through many protocols. Most networking protocols are platform-agnostic, meaning they can be sent and received on any network-capable operating system. If Linux has a Samba client installed, it can access files made available on a Windows share. If Windows has an NFS client installed, it can access Linux / Unix NFS shares.