Some of the software I am using now that has this issue are
iTunes, Internet Download Manager,TwonkyMedia and Virtua Girl HD. All there icons in the system tray disappear when Windows Explorer crashes.
I have a great idea for a new software tool.
A tool that would restore all your system tray icons next to the clock after a Windows Explorer crash!
I really hate when you system tray icons go missing after a Windows Explorer crash!