There are several protocol suites supported by NetBSD. The first one implemented was DARPA's Transmission Control Protocoll/Internet Protocoll (TCP/IP). Shortly afterwards, the Xerox Network System (XNS) was added. The last protocol suites -- parts of them still being implemented -- are the ISO protocol suite, CCITT X.25 and ARGO TP.
Today, TCP/IP is the most widespread of the above. It's implemented on almost any hardware and operating system and it is also the most-used protocol in heterogenous environments. So, if you just want to connect your Amiga running NetBSD to some other machine at home, or you want to integrate it into your company's or university's network, TCP/IP is most probably the right choice.
IPv6 (TCP/IP protocol issue 6, current version IPv4) is under development, several implementations are already available for testing purpose, but no implementation has been incorporated into the official source tree so far.
The Xerox Network System was only implemented at UCB to connect isolated machines to the net, and the ISO-protocols are by far not as widespread as TCP/IP, also their popularity is said to grow.
However, there are no such things as DECnet and Novell's NetWare for NetBSD/amiga, though! These two protocols differ from the protocols mentioned above in that they are proprietary, in contrast to the others, which are well-defined in several RFCs and other open standards.