From the autoconf obsolete macros documentation:
Macro: AC_CANONICAL_SYSTEM
Determine the system type and set output variables to the names of the canonical system types. See section Getting the Canonical System Type, for details about the variables this macro sets.
The user is encouraged to use either AC_CANONICAL_BUILD, or AC_CANONICAL_HOST, or AC_CANONICAL_TARGET, depending on the needs. Using AC_CANONICAL_TARGET is enough to run the two other macros.
From the documentation for the canonical environments:
case $target in
i386-*-mach* | i386-*-gnu*)
obj_format=aout emulation=mach bfd_gas=yes ;;
i960-*-bout) obj_format=bout ;;
esac
Note that the above example uses $target because it's taken from a tool which can be built on some architecture ($build), run on another ($host), but yet handle data for a third architecture ($target). Such tools are usually part of a compiler suite, they generate code for a specific $target.
However $target should be meaningless for most packages. If you want to base a decision on the system where your program will be run, make sure you use the $host variable.
