The pinout designer is a nice tool to keep an overview of the pins.
PCIe/LVDS use both differential pairs and are thus inherently not usable as GPIO.
The SIM card is not connected to the Apalis iMX6 but to the mini PCIe slot.
Resistive Touch comes from a touch controller. The one the Apalis iMX6 can be used as GPIO but I don’t know if there is a driver for that. Even if the driver exist that will require extensive work compared to other options. Also on another Apalis module you may not have that option.
CAN can be used as GPIO, but e.g. on a Apalis T30 the pins are dedicated to CAN, so probably not the best choice.
The parallel camera interface and SPI could both be used for your purpose. You would need to change the device tree to
disable the driver which is currently using the pins
add a new pinctrl node which muxes the pin GPIO
add that new node to an active node, e.g. to the iomuxc node
I will probably use the parallel camera interface pins for that. I’ll find the pins that I want and check its usage, disable them and create a new pinctrl node with them and use them in the driver i need.