If you want to compile oathtool on Windows using Cygwin you can use this small Howto:

1. Install Cygwin
2. Install the following packages into Cygwin (maybe you need less packages, but this is myy actual list grabbed with cygcheck.exe -c) or just try, wait for errors and install the packages based on the error you get._autorebase, _update-info-dir, alternatives, autobuild, autoconf, autoconf2.1, autoconf2.5, automake, automake1.10, automake1.11, automake1.4, automake1.5, automake1.6,
   automake1.7, automake1.8, automake1.9, base-cygwin, base-files, bash, binutils, bzip2, ca-certificates, coreutils, cpio, crypt, cvs, cvsps, cygutils, cygwin, cygwin-doc, dash,
   diffutils, dos2unix, editrights, file, findutils, gawk, gcc-core, gcc-g++, gcc-mingw-core, gcc-mingw-g++, gdb, gettext, git, grep, groff, gzip, ipc-utils, less, libasn1_8, libattr1,
   libbz2_1, libcom_err2, libcurl4, libdb4.5, libexpat1, libffi4, libgcc1, libgcrypt11, libgdbm4, libgmp3, libgnutls26, libgpg-error0, libgssapi3, libheimbase1, libheimntlm0, libhx509_5,
   libiconv2, libidn11, libintl3, libintl8, libkrb5_26, libltdl7, liblzma5, liblzo2_2, libncurses10, libncurses9, libncursesw10, libopenldap2_3_0, libopenssl098, libopenssl100, libpcre0,
   libpopt0, libreadline7, libroken18, libsasl2, libsigsegv2, libsqlite3_0, libssh2_1, libssp0, libstdc++6, libtasn1_3, libtool, libwind0, login, m4, make, man, mercurial, mingw-runtime,
   mingw-w32api, mintty, perl, perl-Error, python, rebase, run, sed, tar, terminfo, texinfo, tzcode, w32api, wget, which, xorg-util-macros, xz, zlib0
3. Download the source from here. I used oath-toolkit-1.12.4.tar.gz
4. Unzip the source to your Cygwin home folder
   tar xzvf oath-toolkit-1.12.4.tar.gz
5. Jump into the newly created folder
   cd  oath-toolkit-1.12.4
6. Execute the following commands
   ./configure
   make
7. Pickup the following files and copy them to a separate folder
   <cygwinbinfolder>\cygwin1.dll
   <cygwinhome>\oath-toolkit-1.12.4\liboath\.libs\cygoath-0.dll
   <cygwinhome>\oath-toolkit-1.12.4\\oathtool\.libs\oathtool.exe
8. You can now run oathtool (without Cygwin) from the newly created folder
   

If you don’t want to compile yourself, you can download my compiled version here (if you trust me!).