This comes up from time to time, the solution is always compile a winelib app with winegcc then use sockets or something to communicate. In your server app you can use windows and linux code mixed together.
If you don't need to use linux APIs in your windows application you can also make a normal windows executable with a windows compiler of your choice. So winegcc/winelib is not a requirement for this style of client/server solution. (You could use winsock to communicate over tcp with the linux application.)
Jan