Execute Shell Commands from Program running in WINE
With newer Wine versions (tested with Wine 1.7.38), you can run a Linux program from within Wine in the following way (here to launch gedit, as an example):
wineconsole cmd
...and from that wine console:
start /unix /usr/bin/gedit
If you want to launch a Linux program directly from within a Windows-application, the following line did work for me:
cmd /c start /unix /usr/bin/gedit
To test this, you can call directly on your Linux console this:
wine cmd /c start /unix /usr/bin/gedit
One important thing to Note: the program you want to start needs to have the executable bit set, otherwise calling it from Wine will fail!
Try this (runs Gnome calculator on my Linux Mint system):
wineconsole cmd
...and from the wine console:
/bin/sh gcalctool
On this general principle, you can also open documents and associate files with a linux app by editing the wine registry. There is a section about it in the wine FAQ:
6.6.3 How do I associate a native program with a file type in Wine?
So you should be able to write shell scripts and call them OK.