Well it has to do with the type of monitor you have. If you have a LCD it should be at 60 hertz, if you have a CRT (tube) it should be above 60, like 70, 80 and so on. If you have paper work for the monitor it should tell you the refresh rates it can handle with what resolution you are using.
If it is a CRT, it is always best to have the refresh rate set for the resolution you are using, say like if your screen is at 1280x1024 you should use a refresh rate of 100 hertz (that is IF the monitor AND video drivers can handle that, it should). In any case "if" you are using a CRT, start off with a refresh rate of 75Hz and see if the Icon (folders) look better to you, just go as far as you need to make the icons look good to you.
If you are using a LCD, make sure the refresh rate is at 60Hz.
Again I am 99% sure your refresh rate is your problem with the way your desk top looks.