ktwebb is correct when referring to NetBios. NetBios/NetBeui, although referred to as a protocol, is really more an interface for applications to communicate.
Since Novell is going away, I would install TCP/IP on the server, since that is likely the primary protocol everyone else is using. I would remove NetBeui and IPX from all my workstations... provdided that nothing was requiring their use. Since Novell is going away, there is no practical reason to keep multiple protocols on any system. Multipl protocols only has the potential to slow down communicatiion responsiveness.
An internal IP address for the W2k box may not be practical. Setting up an internal address for that system alone, would require a gateway be setup between it and the rest of the networked systems need to access this system. Very impractical. Since you already have an establihed TCP/IP network, the W2k system can just be added to that.
since TCP/IP is not running on the WINS server... look in the WINS database and see if it is in fact registering names. Since you say this system cannot communicate with anyone else, I am doubtful that WINS is accomplishing anything.
Once you have this system runnning TCP/IP... it will serve a valuable role as a WINS server.