If you mean custom mapper as in the brewer made it themselves for just that game, then Star Keeper did that.
If you mean a mapper that was developed for sale to homebrewers and not used by Nintendo during the life span, then many. Memblers makes the GT-Rom board. The Incident, Scramble, Spook-o'-Tron, and others used it. I think some of NES Lives boards are new mappers as well.
Edit: GT-Rom Board also for Candelabra Estoscerro, NEScape!, Rollie
Edited: 10/05/2019
at 10:16 AM
by Indo