I managed to get a work around running. For the icon
Code:
[Desktop Entry]
Type=Application
Encoding=UTF-8
Name=EverQuest
Exec=sh -c "cd /media/EverQuest/ && wine eqgame.exe patchme"
Type=Application
StartupNotify=true
Icon=eqicon.png
Terminal=false
I'm still not sure why I have to run it with
cd /media/EverQuest/ && wine eqgame.exe patchme Instead of just
wine /media/EverQuest/eqgame.exe patchme
but at least the icon now works.