There seems to be something called the "Jiffy protocol" used for some fast load systems. I know of the JiffyDOS product, which seems to require replacing ROMs in both the C64 and the drive, but it seems that other programs and devices (such as SD2IEC's GPL'd firmware and SDOS V1.1) also support this.
Is this protocol documented anywhere? How does it work? What libraries, software and hardware (both real and emulated) support faster disk transfers using this?
This is an incomplete answer.
https://www.pagetable.com/?p=1018 references an as-yet-unwritten article about JiffyDOS:
JiffyDOS, a 3rd party ROM patch for computers and drives, replaces layer 2 byte transmission of Standard Serial by using the clock and data lines in a more efficient way. Bus arbitration is unchanged. The controller detects a device’s JiffyDOS support and can fall back to the Standard Serial protocol.
http://www.baltissen.org/newhtm/sourcecodes.htm includes a link to JiffyDOS source, apparently licensed from the original author (Mark Fellows) to Jim Brain (via http://www.go4retro.com/products/jiffydos/) and then to this page, though it should be noted the page explicitly says you should have a JiffyDOS license to use the code: http://www.baltissen.org/files/C64-kerJD.a65
