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NetBIOS is an API (Application Programming Interface) that provides a standard interface for programs to use to communicate over a network. It is not a transport protocol. Most (all?) current (pre-NT5) MS networking relies on NetBIOS connections.

NetBEUI (NetBIOS Extended User Interface) is a very simple transport protocol. It doesn't support any form of routing and all communications are initiated via broadcasts. So it can only be used on a single segment and the volume of broadcast traffic, in a large network, can cause serious performance problems. In general, it is the easiest protocol to implement for full MS networking in a small network and for RAS connections.

IPX/SPX (Internetwork Packet Exchange/Sequential Packet Exchange) is a routable transport protocol. It was made very popular by (and developed by?) Novell and is commonly used by networkable games (unfortunately). The MS version provides a NetBIOS over IPX, so you can provide full MS network functionality with this protocol. IPX/SPX is commonly considered to be a chatty protocol. Like NetBEUI, IPX/SPX is simple to configure (on a single network segment, it usually requires no configuration). However, because IPX/SPX is routable, it isn't limited to a single segment.

TCP/IP (Transport Control Protocol / Internet Protocol) is the common name for a suite of protocols based on IP. IP is a routable transport protocol. MS's implementation of TCP/IP provides NBT (NetBIOS over TCP/IP), which allows full MS networking over TCP/IP. It is, of course, the protocol used on the Internet and is rapidly becoming the transport protocol of choice in many large networks. TCP/IP always requires at least some configuration. In many cases, this configuration can be automated (DHCP, PPP, etc), but someone has to know how to set up the automation.

In general, which protocol(s) you use depends largely on your requirements and your network layout. For long term planning, though, you should probably give serious consideration to implementing TCP/IP. Since TCP/IP (and Internet access) is becoming so popular, you will almost certainly wind up needing to connect to a TCP/IP network, sooner or later.