http://bugs.winehq.org/show_bug.cgi?id=15485
--- Comment #18 from Vorobyov Anton phoenix@mail.ru 2008-09-30 23:39:12 --- There's argument allowing you to launch applications in different virtual desktops, Keyn Thror already mentioned it on official forums:
wine explorer /desktop=0,1024x768 "C:\Program Files\CCP\EVE\eve.exe" wine explorer /desktop=1,1024x768 "C:\Program Files\CCP\EVE\eve.exe"
Notice numbers 0 and 1 after desktop key - these are desktop IDs.