As discussed in this hint, Mac OS X's Finder tends to get very slow when you have a lot of desktop icons. Here's one way to speed things up:
Use the shareware app DeskShade to hide the Desktop, then open a new Finder window and navigate to the Desktop. Organize the files to your liking (preferably with the goal being to remove as many items from the Desktop folder as possible), then unhide the Desktop.
Also of note: as long as DeskShade is hiding the Desktop, the Finder behaves. So you don't ever have to reorganize your Desktop, you just have to keep it hidden most of the time using DeskShade.
[robg adds: If simply hiding the icons on the desktop is an effective fix (I haven't tested that theory), then an alternative solution would be John Haney's free Backdrop, which can be used to hide icons on the Desktop when the floating level is set to "in between." You won't, however, get all of the niceties you get with DeskShade, such as the ability to rotate desktop images, etc.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060310174234350