Remove the program directory right in ~/.wine itself and ignore (or remove) the entry in the applications list from that point onward. It's also recommended that you install any such programs under a different wineprefix so you can test them out and remove them real quick before deciding to install them to the main wineprefix (~/.wine). Running or installing a program under a different wineprefix works as follows: WINEPREFIX=~/directory wine application.exe
