On cold start or warm start the bootloader is a small program that start up the main operating system.
The Openmoko phones can use U-Boot (Openmoko default), U-boot-gena2x (alternative U-Boot) or Qi as bootloaders. Qi and U-boot-gena2x is actively developed (2012), while the Openmoko version of U-Boot is not.
Neo FreeRunner GTA02
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. Note that the NOR bootloader has a size limit of 2 MB for the kernel.
The second NAND resident 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.
The NAND u-boot loader has a size limit of 2 MB for the kernel, but you could rather easily increase it by modifying the u-boot environment.