http://bugs.winehq.org/show_bug.cgi?id=33467
--- Comment #2 from Ken Thomases ken@codeweavers.com 2013-04-27 12:51:59 CDT --- Were you using the Mac driver in Wine 1.5.27? It wasn't the default then, so you would have had to go out of your way and edit a registry key.
The Mac driver was turned on by default in 1.5.28. That, rather than any change to the Mac driver itself, is probably what caused the change. You can check by reverting to Wine 1.5.27 but enabling the Mac driver. That entails creating the registry key HKEY_CURRENT_USER\Software\Wine\Drivers and, within that, create a string value named "Graphics" with the value "mac".
However, I think the behavior is correct. The full-screen program has set its window to have the WS_EX_TOPMOST style, so it's supposed to put it in front of all windows which don't have that style. The Mac driver implements this by putting the window at the "floating window" level. So, only other floating windows can come in front of it.
It is important that the Mac driver implement WS_EX_TOPMOST as a floating window because not all such windows are full-screen. For example, an app might create a topmost "palette" that should be visible and accessible even in front of other apps. It is arguably a bug in XQuartz that it doesn't support this mode of operation.
A relevant question, which I'm not sure you can answer, is what those same full-screen programs do on Windows when you Alt-Tab away from them. If they change their window's style, minimize the window, hide it, or something like that, then we should make sure that they do the same under the Mac driver. However, many full-screen Windows programs either don't allow you to Alt-Tab away or don't behave any better than what you're describing.
As a possible feature request, we can consider adding a registry key that would change the behavior of the Mac driver so that it demotes windows back to normal when you switch to another app, but the default should probably still be to honor the window style.
Lastly, as a workaround, you can hide the relevant Wine process. This is complicated by the fact that the Mac driver doesn't currently put a "Hide" item in its Mac application menu. That's on the to-do list for the Mac driver. In the meantime, you can use the Dock menu or the Command-Tab application switcher to hide an app (while the switcher is showing, highlight the app, and press the H key).