anshul@green /cygdrive/c/Users/anshul/Project/ffmpeg
$ ./configure --arch=x86 --target-os=mingw32 --cross-prefix=x86_64-w64-mingw32- --pkg-config=pkg-config --enable-gpl --enable-libx264 --disable-optimizations
ERROR: libx264 not found

If you think configure made a mistake, make sure you are using the latest
version from Git.  If the latest version fails, report the problem to the
ffmpeg-user@ffmpeg.org mailing list or IRC #ffmpeg on irc.freenode.net.
Include the log file "config.log" produced by configure as this will help
solve the problem.

anshul@green /cygdrive/c/Users/anshul/Project/ffmpeg
$ pkg-config.exe --list-all
gsettings-desktop-schemas gsettings-desktop-schemas - Shared GSettings schemas for the desktop, including helper headers
x264                      x264 - H.264 (MPEG4 AVC) encoder library
uuid                      uuid - Universally unique id library
python-2.7                Python - Python library

anshul@green /cygdrive/c/Users/anshul/Project/ffmpeg