Difference between Unix and DOS/Windows?

Can anyone tell me what are the basic differences between Unix and DOS/Windows file systems?

Please also explain why programs written on unix don't run under windows/dos and vice versa.

Thanks a lot

Unix File System: http://www.cs.wlu.edu/labs/unix/unix.html

A simple answer for the second question is that applications rely on functionality provided by the OSes API to do certain things, like access a file or create a window. There are things like cygwin or wine or even java to get around this.