protocols are defined ways for programs to interact with each other, and key building blocks of the IndieWeb.
See specifications for a list of protocols that are in wide use among the IndieWeb.
Tantek noted some trends in protocol design in an informal stream of consciousness chat (late night PDT rant 2021-06-28). Editing for readability, some implied bits made more explicit, and some tone (in progress)
IRC is of the same era as SMTP, where those designing / architecting inventing it presumed good will by participants, due to unawareness by the inventors of swimming in their highly privileged waters.
Sure they (IRC inventors/implementers) tried to patch it after the fact with various *SERVs, human moderators etc. but it was all to patch architectural designs based on flawed assumptions of human nature.
However by virtue of being of that era, IRC/SMTP were also of the modem era, where every byte counted, and thus when the protocols "worked" (were used by good faith human actors), they were EXTREMELY efficient/fast and reliable, at least at a byte level, because they were designed to work / recover over bad / slow / unreliable network connections.
My earliest memories of XMPP were with just how slooooooooow its implementations were to do basic things like connect, log on, latency of message sending/receiving. Nevermind complete lack of basic interop (images, file transfers etc., even SMTP got those right).
Matrix (by way of its clients) is even slooooooooooooower. I tried keeping a tab open to a Matrix server with many channels and gave up after it would leak memory worse than any other web application, and was perhaps the most inefficient use of JS to move around a bunch of small bits of text that I've ever seen.
There really is no excuse for making sending small bits of text back/forth that slow. I don't even want to know the overhead %, nay, multiplier that Matrix has for sending a sentence of text.
For modern protocols, we need a combination of modern knowledge of just how bad humans are by default in social systems (power asymmetries, trolls etc.) and folks that have experience designing (and implementing!) protocols that very efficiently (with low-latency) send small bits of text back/forth.
One more thing, not only do we not have folks that have experience (and desire to keep) designing very (byte for byte) efficient protocols, we have the COMPLETE OPPOSITE.
A bunch of folks are malincentivized by their ICOs to design VERY INEFFICIENT protocols that burn ridiculous amounts of power & time to perform operations. This is the worst of both worlds, the cryptocurrency/blockchain advocates appear to act in ways and make proposals that show complete ignorance & neglect of anyone's safety but their own cryptocurrency accounts (and even those are also compromised due to misuse of SMS).
See: format#FAQ for format vs protocol questions.