AMMDI is an open-notebook hypertext writing experiment, authored by Mike Travers aka mtraven. It's a work in progress and some parts are more polished than others. Comments welcome! More.
The Harlan Ellison story Repent Harlequin said the Ticktockman
That scene in The Sopranos where they try to shake down a Starbucks
Most of Seinfeld and Curb Your Enthusiasm
The Wire (and really all police procedurals, or all workplace procedurals, or maybe almost all drama whatsoever)
Deadwood is pretty explicitly about protocols; the characters are very aware of protocols, the main drama is about the imposition of protocols (capitalism vs government vs lawlessness).
Various minor moments: Bullock and Utter commenting on the absurditities in trying to arrange these male-male social occasions ("maybe I should of brought posies"). The open discussion of the "bribe sheet".
Milch's earlier show NYPD Blue, a better-than-average cop show, pretty protocolized as the detectives try and do their work within permissible lines. The IAB (rat squad) is the hated enemy because they are cops to cops.
The Wire on the other hand is about governance collapsing, how individuals deal with a dysfunctional instutiton and its protocols. They invent new ones. Stringer Bell's arc is trying to replace gangser protocol with capitalism, and failing. "Is you taking notes on criminal fucking conspiracy"?
Bruce Sterling’s 1998 novel Distraction has a number of different aspects involving protocols:
the opening scene is a flash mob swarming attack on a bank
the main character is a political operative who is trying to resucitate failing social institutions by protocol-hacking them
one of his clients is an architect/designer who developed a distributed, protocolized construction technology which figures in the plot
The Bruce Sterling story Maneki Neko has a network-mediated gift economy that exists as a kind of subversive subculture within capitalism. This story also involves a conflict between protocol systems. I officially declare this the most protocol story ever.