Gnome is quite a nice desktop environment and as with all desktops they tend to put on weight and gain bloat.
From time to time you need to get rid of excess and unused items. Desktop icons for example. I rarely use them, and mostly they are buried beneath an open application. So, its time for them to go.
To remove desktop icons in Gnome, do:
Applications > System Tools > Configuration Editor
apps > nautilis > desktop
Uncheck the icons you want gone and voila.