Multiplayer
Multiplayer can refer to 4P-capable games like Kizuna Encounter - Super Tag Battle using the NEO-FTC1B board, or multi-system cable-linked games like League Bowling, Riding Hero and Thrash Rally.
The linkable cartridges had a dedicated HD6301 MCU and used a 3.5mm stereo jack cable to communicate with each other.
Protocol
Data is transmitted by the HD6301 using its SCI module, a data frame is composed of a start bit, 8 data bits then a end bit. Transmitted data is NRZ encoded, data rate seemingly is 62,500 bauds. See source on MCU page.
MVS Multiplayer
MVS carts are fitted with two 3.5mm jack plugs to daisy chain up to 4 systems. Cabinet ID is setup by hard dips, as well as comm enabling.