There are also specs which have further refinements of replies, such as "agree" or "disagree", including [WWW]IBIS and Annotea: (RDF schema that defines "seeAlso", "Agree", "Disagree", and "Comment")

local vs. distributed

MessageThreading can be implemented as "local to publishing system", where all resources are guaranteed to be consistent and available, and "distribute", where resources cross system boundaries and individual links are less likely to be available. The logical relationships remain the same, but the implementation can be more difficult.

"parent" vs. "in-reply-to"

Discussion of the terms "parent" and "in-reply-to" concerning message threading, mostly centering around "generic" vs. "specific".