The $(VARIABLE) syntax is usually preferred, because it is possible for the
user to override it at "make" time, whereas @VARIABLE@ is hardwired at
"configure" time.
There was some discussion of this on bug-gnulib@gnu.org:
http://comments.gmane.org/gmane.comp.lib.gnulib.bugs/18588
The summary is that Bruno Haible sometimes prefers @VARIABLE@ but most
others generally prefer $(VARIABLE), for the reason given above.