Mask ROM pinout
8kB / 16kB / 32kB / 64kBytes (28pin) ROMs
Nintendo used by default JEDEC standard compatible pinouts for all their mask ROMs of 64 kBytes and below (but some particular boards might be exceptions !). Names [in brackets] applies when the corresponding address pin is unused. On boards where an adress pin is never used (for example, A15 is never used on NROM boards as the ROM can't be greater than 32k), what is in brackets connects to the unused pin.
For some unknown reasons, unused address lines on smaller ROMs had to be put to +5V, as Nintendo made different boards for each size (as opposed to place EPROMs of different sizes into the same slot). Some boards, such as CNROM, features solder pads in order to force those pins to +5V though. As Nintendo liked to use Mask ROMs from various manufacturers, apparently unused pins could be either not connected or additional active high CE enable lines. This would ensure that if Nintendo would order mask ROMs with additional enable lines that aren't used, they could place them on the board without having the fear of having them disabled accidentally.
This doesn't apply to CHR ROMs - i.e. a smaller ROM can always fit a slot made with a larger ROM in mind. Probably as the game will work if the ROM is "accidentally" disabled before the first write to CHR bankswitching registers.
27C64/128/256/512 EPROM pinout ---_--- [+5V] A15 - |01 28| - +5V A12 - |02 27| - A14 [PGM] A7 - |03 26| - A13 [NC] A6 - |04 25| - A8 A5 - |05 24| - A9 A4 - |06 23| - A11 A3 - |07 22| - /OE A2 - |08 21| - A10 A1 - |09 20| - /CE A0 - |10 19| - D7 D0 - |11 18| - D6 D1 - |12 17| - D5 D2 - |13 16| - D4 GND - |14 15| - D3 -------
128/256/512 KBytes (28/32pin) ROMs
Nintendo used the standard pinout for (extremely rare) prototype boards intended to take a 27C010/020/040 EPROM. But retail Game Paks made by Nintendo have mask ROMs with a different pinout which is not compatible. This pinout, with reshuffled enable lines and higher address lines, allows a 32-pin hole to take a 28-pin 128 KiB PRG ROM in pin 3 to pin 30.
For games using 256 KiB and larger ROMs, other companies producing Famicom or NES boards used either epoxy blobs or standard EPROM pinout. But games with 128 KiB of PRG were more often in a 28-pin package than not.
On Nintendo's boards where PRG A18 is never used, pin 2 is connected with pin 22.
Nintendo's MMC5 boards use the same pinout for both PRG and CHR ROMs, and even 128 KB PRG ROMs are 32-pin so they can have a VCC pin.
CHR ROM, PRG ROM, and 27C010/020/040/080 EPROM pinouts compared MMC5 CHR PRG EPROM EPROM PRG CHR MMC5 ---_--- A17 A17 [+5V] A17 [VPP] A19 - |01 32| - +5V A18 /OE A18 [/CE] A16 - |02 31| - A18 [PGM] +5V /CE /CE A15 - |03 30| - A17 [NC] +5V +5V A19 A12 - |04 29| - A14 A7 - |05 28| - A13 A6 - |06 27| - A8 A5 - |07 26| - A9 A4 - |08 25| - A11 A3 - |09 24| - /OE A16 A16 A16 A2 - |10 23| - A10 A1 - |11 22| - /CE GND A0 - |12 21| - D7 D0 - |13 20| - D6 D1 - |14 19| - D5 D2 - |15 18| - D4 GND - |16 17| - D3 ------- PRG and CHR pins are listed only if they differ from EPROM.
Here is a list of multiple variants of Nintendo's pinouts above. Only a couple of enable pins typically differs (which are shown in bold).
Nintendo RROM CHR ROM pinout - 8 KBytes (28pin)
This particular board is functionally identical to NROM but with a strange CHR pinout :
RROM Non-standard 64-kbit CHR pinout ---_--- A7 - |01 28| - +5V A6 - |02 27| - A8 A5 - |03 26| - A9 A4 - |04 25| - A12 A3 - |05 24| - /CE +5V - |06 23| - NC +5V - |07 22| - /OE A2 - |08 21| - A10 A1 - |09 20| - A11 A0 - |10 19| - D7 D0 - |11 18| - D6 D1 - |12 17| - D5 D2 - |13 16| - D4 GND - |14 15| - D3 -------
Nintendo SROM CHR ROM pinout - 8 KBytes (24pin)
This particular board is functionally identical to NROM but the CHR uses a 24-pin 8KB ROM with pinout very similar to the 27C32:
SROM 23C62/64 JEDEC-Standard 64-kbit CHR pinout ---_--- A7 - |01 24| - Vcc A6 - |02 23| - A8 A5 - |03 22| - A9 A4 - |04 21| - A12 A3 - |05 20| - /OE A2 - |06 19| - A10 A1 - |07 18| - A11 A0 - |08 17| - D7 D0 - |09 16| - D6 D1 - |10 15| - D5 D2 - |11 14| - D4 Gnd - |12 13| - D3 -------
With only one output enable, the board synthesizes the signal (/OE = PPU A13 + PPU /RD) using two transistors and a resistor.
This board uses three 23C62, 8 KBytes, 24 pin MASK ROMs (two as PRG-ROM and one as CHR-ROM) and a few discrete elements for an address decoder 
Nintendo AOROM PRG ROM pinout - 128/256/KBytes (32pin)
Very slight variant of the standard PRG-ROM pinout above, where an additional active high enable line is used to prevent bus conflicts.
---_--- A17 - |01 32| - +5V /CE - |02 31| - CE (R/W) A15 - |03 30| - +5V A12 - |04 29| - A14 A7 - |05 28| - A13 A6 - |06 27| - A8 A5 - |07 26| - A9 A4 - |08 25| - A11 A3 - |09 24| - A16 A2 - |10 23| - A10 A1 - |11 22| - /CE A0 - |12 21| - D7 D0 - |13 20| - D6 D1 - |14 19| - D5 D2 - |15 18| - D4 GND - |16 17| - D3 -------
Japanese After Burner connects two such 128 kB mask roms in parallel (pin 2 = PPU /RD, pin 22 = SS4-CHR-/CE, pin31 = SS4-CHR-A17), which implies that one of them needs to have pin 31 active low and the other active high. 
- /CE, /OE
- The ROM will output data at address A on pins D only if all its CE (chip enable) and OE (output enable) pins are active (CE active high, /CE active low). /CE is sometimes called /CS (chip select). A memory responds faster to /OE than to /CE but draws less current while /CE is not asserted.
- PGM, VPP
- Used only during EPROM programing / erasing process.
See Cartridge connector for other signals descriptions.
Converting a donor board
To convert a cartridge board to accept EPROM:
- Compare the pinout of your EPROM to the mask ROM pinout expected by the board.
- Lift any pins whose signals differ.
- Solder short wires to the corresponding holes.
- Solder down the memory or socket with the pins that do not differ.
- Solder each lifted pin to the hole with the same signal.