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)
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.