I have Ubuntu 12.10 with Nautilus 3.4.2.
After installing wine "apt-get install wine" are exe files still associated with the archive manager.
In previous versions of ubuntu I've always right clicked on the file, choose Properties > Open with > Select an application to open ... > Wine.
But since version 12.04 Wine in Programs menu is missing.
I tried it on a laptop and PC, version 12.04 and 12.10.
I found a workaround:
http://vazhavandan.blogspot.cz/2012/12/nautilus-342-open-as-administrator-hack.html
But I wanted to find a correct solution, Im installing ubuntu to users, and I'd like at everything works as it should.
Thx