Some packages, notably GNU GCC and GNU gdb, have a build environment originally written at Cygnus Support (subsequently renamed Cygnus Solutions, and then later purchased by Red Hat). Packages with this ancestry are sometimes referred to as "Cygnus" trees.
A Cygnus tree has slightly different rules for how a Makefile.in is to be constructed. Passing -cygnus to automake will cause any generated Makefile.in to comply with Cygnus rules.
Here are the precise effects of -cygnus:
Info files are always created in the build directory, and not in the source directory.
texinfo.tex is not required if a Texinfo source file is specified. The assumption is that the file will be supplied, but in a place that Automake cannot find. This assumption is an artifact of how Cygnus packages are typically bundled.
make dist is not supported, and the rules for it are not generated. Cygnus-style trees use their own distribution mechanism.
Certain tools will be searched for in the build tree as well as in the user's PATH. These tools are runtest, expect, makeinfo and texi2dvi.
-foreign is implied.
The options no-installinfo and no-dependencies are implied.
The macros AM_MAINTAINER_MODE and AM_CYGWIN32 are required.
The check target doesn't depend on all.
GNU maintainers are advised to use gnu strictness in preference to the special Cygnus mode. Some day, perhaps, the differences between Cygnus trees and GNU trees will disappear (for instance, as GCC is made more standards compliant). At that time the special Cygnus mode will be removed.