The bootloader is a small program to start up the main operating system. The Openmoko phones can use U-Boot or Qi as bootloaders. Qi is actively developed, while the Openmoko version of U-Boot is not.
The Neo FreeRunner has two bootloaders. The NOR Flash contains a version of U-Boot which cannot be modified. Therefore it is always available as a fallback, and the second bootloader can be modified without any risk. This bootloader can be booted into by pressing and holding the AUX button and then pressing the Power button.