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If somebody else had ideas about using old APM1's and soon to become old APM2's for some different purpose than autopiloting - probably you will want to connect some hardware, right?

I have gone through what I could find of documentation, and measured what was not documented.

Here is a brief overview of the connections on APM1 and APM2 that are available, once external servo wires and external (voltage, current, airspeed etc.) sensors are removed. Especially the APM1 "oilpan" shield has many routed but unused pin connections.

Not included are: UARTs, SPI and I2C, as they are pretty obvious.

External ports APM1:

Where nothing else is mentioned, connections are to the ATMEGA2560.

APM1 PWM inputs:

PWM inputs IN0..IN8: PD0..PD7 on the PPM encoder ATMEGA328p. They are hardly useful for general purpose IO, as there is only the single PPM wire to communicate to the ATMEGA2560 via.

PL0 (ICP4) is the ATMEGA1280/2560 PPM input pin.

APM1 PWM outputs:

PWM output OUT1: PL4 (OC5B) via 220R resistor
PWM output OUT2: PL5 (OC5C) via 220R resistor
PWM output OUT3: PB6 (OC1B) via 220R resistor
PWM output OUT4: PB7 (OC1C) via 220R resistor
PWM output OUT5: PH5 (OC4C) via 220R resistor
PWM output OUT6: PH4 (OC4B) via 220R resistor
PWM output OUT7: PE5 (OC3C) via 220R resistor
PWM output OUT8: PE4 (OC3B) via 220R resistor
Unknown pin on oilpan: PB5 (OC1A)
Unknown pin on oilpan: PE3 (OC3A)

APM1 Analog:

A0: PF0 via 10k resistor

A1: PF1 via 10k resistor
A2: PF2 via 10k resistor
A3: PF3 via 10k resistor
A4: PF4
A5: PF5
A6 ("expansion port"): PF6
A7:("expansion port"): PF7

APM1 Other:

PD0, PD1 are I2C. PD2, PD3 are UART1. PE0, PE1 are UART0.
PG0 is SW1 the unused button (AFAIK completely ignored in Ardupilot soft).
PG1 is the "slider switch" (AFAIK completely ignored in Ardupilot soft).
PORTC is routed to Oilpan (JP14). PC0, PC1, PC2 are the three LEDs.

Which port is driving / did drive the relay? It is Arduino Pin47, PL2?

PE6, PE7 and PL6, PL7 are the Oilpan DIP switches (AFAIK completely ignored in Ardupilot soft).

External ports APM2:
Where nothing else is mentioned, connections are to the ATMEGA2560.

APM2 PWM inputs:

PWM inputs IN0..IN8: PB0..PB7 on the PPM encoder ATMEGA8U2. There is a serial connection between ATMEGA8U2 and ATMEGA2560, so a custom firmware on 8U2 could forward (slow) data to/from 2560 from/to the port.

PL1 (ICP5) is the ATMEGA2560 PPM input pin.

APM2 PWM outputs:
PWM output OUT1: PB6 (OC1B) via 220R resistor
PWM output OUT2: PB5 (OC1A) via 220R resistor
PWM output OUT3: PH5 (OC4C) via 220R resistor
PWM output OUT4: PH4 (OC4B) via 220R resistor
PWM output OUT5: PH3 (OC4A) via 220R resistor
PWM output OUT6: PE5 (OC3C) via 220R resistor
PWM output OUT7: PE4 (OC3B) via 220R resistor
PWM output OUT8: PE3 (OC3A) via 220Rk resistor

PB7 = OC1C (NOTE Ch.9 out is not supported in firmware!!!)

APM2 Analog:
A0-A7: PF0..PF7 = ADC0..ADC7 (used for analog signals)
A8: PK0 = ADC8
A9: PK1 = ADC9 or PB7 (default) jumper selectable. PB7 via 1k resistor.
A10: PK2 = ADC10 or PL4 (default) jumper selectable. PL4 via 1k resistor. PL4 = OC5B
A11: PK3 = ADC11 or PL5 (default) jumper selectable. PL5 via 1k resistor. PL5 = OC5C