Spark could have an option to indicate incoming messages in system tray (flashing, changing icon, etc.). This could be especially useful with burden taskbars, when there is few rows of windows and new chat window are not visible. Also, this could be a workaround for "bring window to front" bug, when chat windows are not flashing in taskbar. Could be optional in Notifications preferences.
this feature has a high voting in recent poll:
another idea http://www.igniterealtime.org/community/message/187164#187164
there could be an additional option to not open new windows for new messages, but just show flashing icon in systray and open new window only when one clicks on that icon.