Cross-platform programs are sometimes distributed as .tar.gz for the Unix version and .zip for the Windows version. This makes sense when the contents of each must be different.
If, however, the contents are going to be the same, it would be simpler to just have one download. Windows prefers .zip because that's the format it can handle out of the box. Does it matter on Unix? That is, I tried today unzipping a file on Ubuntu Linux, and it worked fine; is there any problem with this on any current Unix-like operating system, or is it okay to just provide a .zip file across the board?