If one wanted to write a app in C for MOS but only wanted it to run on a MOS enabled system... how would one accomplish this?

You mean that dont work on AmigaOnes?
just in Pegasos?

I'm not going to put it like that.. I'm just saying if you're running MOS it'll work.

GCC proggy.c -O2 -D__MORPHOS__ -noixemul -o proggy

:)

Just compile MorphOS native PPC binary only and dont give source code anyone

MorphOS native binaries wont run in OS3 or OS4 at all - however more supported platforms mean more happy users.

if you still code in 68k (E, BlitzBasic2, SAS/C, whatever):

if ( !(FindResident("MorphOS")) )
{
ColdReboot();
}

If you check the SDK docs, there are MOS-only API calls in there. Use them, I'd suggest.

Install the MOS SDK and use its gcc or get vbcc to compile MorphOS executables.

Then, that's true there are differencies between AmigaOS and MorphOS. This last one have new functions (Intuition, process, ...) and if you use this specific stuff without taking care of manage an AmigaOS part of code that does the same thing, you will have MorphOS only programs.

Not difficult to support both though ...