Each time the machine refreshes the desktop, it is visually having to update all the file information that is stored on the desktop - each time, especially image files with preview icons. It wouldn't need to do that if they are stored away in a folder. It is just one aspect that can cause slower...
Some Mac's, MacBookPro's and iMac's can run too hot slowing the processors down. There is a app that gives you all the temperature readings, and if you google 'iMac running too hot' there are tips on how to keep it cool.
Run Activity Monitor in the corner somewhere, this can really help...