Even new codes, like DFTB+ or Quantum Espresso, are written only for Linux / UNIX environment, and no complied version available for Windows PCs. There are several legacy codes in computational chemistry which was written in FORTRAN, and never were translated to other language. You can have (free) c,c++,fortran etc.It means, you can directly read your output files on the Linux machine, and dont need to FTP to your PC for a short look. You also can run Molden on a Linux machine, and have the graphical output on your PC. A good example is Molden, which needs X for the graphical interface. If you are running Unix/Linux programs with graphical interface then you generally need this.
The point to remember: you can somehow run Linux-ish programs on your Windows PC with it. If you don’t understand what this exactly means, then just believe me, that is it USEFUL and FREE, which is generally pretty good from a software nowadays.
Cygwin ( link) is a UNIX-like environment that can run in Windows (any 32 and 64 verision), so it allows running GNU codes and X.
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