gistfile1.txt

First I've downloaded ode from here: 
  http://sourceforge.net/projects/opende/files/ODE/0.12/ and extracted it in my e:\p under e:\p\ode-0.12

Then I did (from cmd.exe)
  bash --login -i

$ cd /cygdrive/e/p/ode-0.12
$ ./configure
checking build system type... x86_64-unknown-cygwin
checking host system type... x86_64-unknown-cygwin
checking for a BSD-compatible install... /usr/bin/install -c
.... lots of lines printed out (configure is rather slow under cygwin)
.... then at the end it printed out
.....
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for clock_gettime... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/testsuites/Makefile
config.status: creating src/testsuites/cu/Makefile
config.status: creating src/ccd/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
Configuration:
  Build  system type:      x86_64-unknown-cygwin
  Host   system type:      x86_64-unknown-cygwin
  Use double precision:    no
  Use drawstuff:           Win32
  Demos enabled:           yes
  Use OPCODE:              yes
  Use GIMPACT:             no
  Custom colliders:
        cylinder-cylinder: none
        box-cylinder:      default
        capsule-cylinder:  none
        convex-box:        none
        convex-capsule:    none
        convex-cylinder:   none
        convex-sphere:     default
        convex-convex:     default
  Is target a Pentium:     yes
  Is target x86-64:        yes
  Use old opcode trimesh collider: no
  TLS for global data:     no
  Enable debug error check: yes
  Headers will be installed in ${prefix}/include/ode
  Libraries will be installed in ${exec_prefix}/lib
  Building in directory    /cygdrive/e/p/ode-0.12
  
$ make -j8

# (-j8 means use 8 threads to compile it, if you have less cpu's on your machine do -j2, or just omit -j, just do make)
# now wait to compile

...

make[3]: Leaving directory '/cygdrive/e/p/ode-0.12/tests/UnitTest++/src'
make[3]: Entering directory '/cygdrive/e/p/ode-0.12/tests/UnitTest++'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/cygdrive/e/p/ode-0.12/tests/UnitTest++'
make[2]: Leaving directory '/cygdrive/e/p/ode-0.12/tests/UnitTest++'
make[2]: Entering directory '/cygdrive/e/p/ode-0.12/tests'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/cygdrive/e/p/ode-0.12/tests'
make[1]: Leaving directory '/cygdrive/e/p/ode-0.12/tests'
make[1]: Entering directory '/cygdrive/e/p/ode-0.12'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/cygdrive/e/p/ode-0.12'

# At this point, you can try running it directly from the place you've built it:
# Let's look for some exe files:

$ find . | grep exe$
./build/premake4.exe
./drawstuff/dstest/dstest.exe
./ode/demo/demo_basket.exe
./ode/demo/demo_boxstack.exe
./ode/demo/demo_buggy.exe
./ode/demo/demo_cards.exe
./ode/demo/demo_chain1.exe
./ode/demo/demo_chain2.exe
./ode/demo/demo_collision.exe
./ode/demo/demo_convex_cd.exe
./ode/demo/demo_crash.exe
./ode/demo/demo_cyl.exe
./ode/demo/demo_cylvssphere.exe
./ode/demo/demo_feedback.exe
./ode/demo/demo_friction.exe
./ode/demo/demo_gyroscopic.exe
./ode/demo/demo_heightfield.exe
./ode/demo/demo_hinge.exe
./ode/demo/demo_I.exe
./ode/demo/demo_jointPR.exe
./ode/demo/demo_jointPU.exe
./ode/demo/demo_joints.exe
./ode/demo/demo_kinematic.exe
./ode/demo/demo_motion.exe
./ode/demo/demo_motor.exe
./ode/demo/demo_moving_convex.exe
./ode/demo/demo_moving_trimesh.exe
./ode/demo/demo_ode.exe
./ode/demo/demo_piston.exe
./ode/demo/demo_plane2d.exe
./ode/demo/demo_slider.exe
./ode/demo/demo_space.exe
./ode/demo/demo_space_stress.exe
./ode/demo/demo_step.exe
./ode/demo/demo_tracks.exe
./ode/demo/demo_trimesh.exe

$ ode/demo/demo_buggy.exe
Press:  'a' to increase speed.
        'z' to decrease speed.
        ',' to steer left.
        '.' to steer right.
        ' ' to reset speed and steering.
        '1' to save the current state to 'state.dif'.
      
# Success (3D window popping out)

# NOW MAKE SURE YOU HAVE X11 WINDOWS RUNNING (I have mine automatically running in Startup), but you can run your manually from cmd.exe by typing startxwin

C:> startxwin