I am using KDE on Fedora 16 and when I close down an application my desktop often goes really slow for a while (perhaps 30 seconds to a few minutes). It's like the program hangs when shutting down and the desktop does not repaint itself for a while. Then suddenly the problem ends and it's back to being snappy/responsive.

I have a new AMD processor with three cores and 8 GB of RAM so it shouldn't be a slow system. I am also running the OS off of a SSD. The df command shows plenty of disk space left for all mount points.

I am using a fresh install of Fedora 16 and KDE (only about a week old) and it seems that I have had this problem right from when I installed the OS and desktop.

no real idea, try disabling desktop effects (alt+shift+F12) and closing an app

Also, can you verify that no swapping is occurring? (I know this sounds strange, but the Linux kernel will swap under the most unusual circumstances)