Retrocopy encourages reporting unsupported NES mappers, so here are the ones I've found until now, as for v0.666:
Mapper #33 - Bubble Bobble 2 (J)
Mapper #64 - Shinobi (Tengen)
Mapper #65 - Spartan X 2 (J)
Mapper #69 - Batman - Return of the Joker (U)
Mapper #71 - Mig-29 Soviet Fighter (Unl)
Mapper #90 - Mickey Mania 7 (Unl)
Mapper #91 - Mortal Kombat II (Unl)
Mapper #141 - Super Pang (Sachen) (BTW, does ANY NES emulator run this one?)
Mapper #187 - Street Fighter II - The World Warrior (Unl)
Mapper #210 - Mortal Kombat 2 (Unl)
This list is by no means complete. My guess is that also most XXX-in-1 carts won't work, but IMHO those are not as important as individual games.
I think this thread has more chances of being of use for the authors if users contribute with more mappers, providing as I did the carts that use them to simplify reference.