How do I implement a userspace bootloader on Arduino Due? Is it possible to use a custom bootloader, that loads and executes a main program stored for example on an SD card? The idea is to make it possible to update the Arduino remotely.

I tried this with a bootloader, which writes the program into the flash storage with a 32KB offset and then uses a function pointer with that address (0x88000) to continue execution there. The 0x80000 is as far as I am informed the address offset of the flash storage. It can be written on Due boards with this library: https://github.com/sebnil/DueFlashStorage. The problem was that this just hasn't worked, the Arduino simply stopped responding after the function pointer being executed. I would appreciate any information or hints on this topic.
The guys at Phoenard did just that with an AVR2560. They wrote a bootloader that loads and saves FLASH memory from/to the Micro-SD card. You can save HEX files on an SD card and then load one of them in the FLASH memory and run it.