Have a look at http://blogs.freescale.com/2012/06/26/codewarrior-tool-tip-8-extending-the-build-system/
So this could be used say to run a script/batch file which changes a source file and increments the build number.
Another possibility is to use the burner which would modify the S19/binary file. Again either with a .bbl or with a post build step:http://mcuoneclipse.wordpress.com/2012/09/27/s-record-intel-hex-and-binary-files/
What I'm using as a build identification is as well the __DATE__ and __TIME__ compiler macros. This is not a build number, but gives date and time of the build in a string. I use it like this in my FSShell component:
FSSH1_SendStatusStr((const unsigned char*)"Firmware", (const unsigned char*)__DATE__, io->stdOut);
FSSH1_SendStr((unsigned char*)" ", io->stdOut);
FSSH1_SendStr((unsigned char*)__TIME__, io->stdOut);
FSSH1_SendStr((unsigned char*)"\r\n", io->stdOut);
The output of this you can see n the last screenshot in http://mcuoneclipse.wordpress.com/2012/08/05/a-shell-for-the-freedom-kl25z-board/.
Hope this helps,
Erich