I used to have really messy desktops. In my doze days I could never be bothered removing shortcuts.
Because they were there I used them and they became standard. Recently I've made a big effort to switch to using panels.
Even my XP boot looks clean now. I'll get a shot of that now.
//edit - here it is.
I've got 2 hidden panels in both bottom corners with the systray a menu with the apps I actually use and start button in them. The three tabs at the top give me My Computer/Documents/etc., A volume control and the time. I did most of this out of boredom though. I only play games in XP and I used to kill explorer for that anyway.
//edit2 - of course I use uTorrent as well. How does that work in Linux. Are you using Wine, Cedega or Crossover.