Big endian seemssystems seem to be on it'stheir way out. Many of the traditional unixes used big endian but they have been in decline for years in favor of linux on x86.
arm is bi-endian but the big endian variant seems to be rarely seen.
mips exists in both variants. Afaict the big endian variant is mostly seen on networking applicances (for historical reasons internet protocols generally use big endian).
ppc was traditionally big endian with some parts supporting both endians but IBM seems to now be pushing little endian mode for 64-bit ppc (they recently pushed ppc64el ports into Debian and Ubuntu).
sparc is normally big endian but again seems to be in decline.
If you are implementing an existing protocol then obviously you have to follow it's specifications. If you want the IETF to bless your new protocol then big endian is likely to be easier because that is what they already use in their existing protocols but IMO for a new "greenfield" protocold design little endian is the way to go.
You can either put in macros from the start which will be no-ops on little endian systems or you can not bother until/unless you need to port to a big endian system.