Comment 14 for bug 635223

Installation of Wine package provides some .directory files in ~/.local/share/desktop-directories - these provide folders for the "wine" and "Programs" namespace. However, these are duplicated by the .directory files the package itself provides so they should get ignored (the package provides them so the Wine folder appears after installing the package but before running Wine, as well as to populate the initial links such as Browse C: Drive)

After installing programs, Wine then adds .desktop files in subfolders within ~/.local/share/applications/wine/Programs. These don't contain a category, however Gnome is smart enough to put them in the appropriate folder, because it learns this via their path.

In the past I seem to remember a bug or two about Wine links just appearing entirely within Applications->Other (rather than their proper subfolders, eg Wine->Programs->World of Warcraft), presumably because the directories stopped being read.