phoenix said:src.conf is only used by the buildworld process, and is a simple list of things you don't want to build/install.
make.conf is used by the ports tree, the buildworld process, and (I believe) any make process that uses the FreeBSD /usr/share/Mk infrastructure.
IOW, make.conf is like a global configuration file for make, and src.conf is a local configuration file for the source tree.
First of all, the initial list of specifications will be read from the
system makefile, sys.mk, unless inhibited with the -r option. The stan-
dard sys.mk as shipped with FreeBSD also handles make.conf(5), the
default path to which can be altered via the make variable __MAKE_CONF.