Keep in mind that this is just my opinion and that I've got literally zero experience with naming CPAN modules...
First of all, I'd advise "Net::3MSIP2::Server". It doesn't roll of the tongue nicely, and the fact that the protocol was created by 3M is largely irrelevant in practice. "Library::Net::SIP2" would work, but I think there's potential for confusion there: when you don't already know SIP2 is used by actual libraries, "Library"'d make you think that the module is a wrapper for a library in the computing sense, say libsip2 or libnetsip2, whatever that might do. Well, it sure would make me think that, at least!
I think "Net::SIP2::Server" is a good name; it avoids all these problems and immediately tells you what you need to know about the module: it's for network communication; specifically, it's for a protocol/service/... called SIP2; and even more specifically, it's for writing a SIP2 server. You don't need to know anything about the protocol or its applications to be able to tell.
(BTW, regarding the "Server" bit -- that's obviously just my interpretation, but I take it the module is for building a SIP2 server, right? If not, I'd obviously suggest naming it something else, say "Net::SIP2" if it's generic code intended for use by both clients and servers, or if the SIP2 protocol itself doesn't distinguish between clients and servers.)
