Update: read second comment
I recently upgraded to Ubuntu Jaunty Jackalope, and have experienced a much slower response of my desktop since. The problem seems to be with Intel GMA chips, as my computer has. The reason for the poor performance is that Canonical Ltd. decided not to include the UXA acceleration in Jaunty, for stability reasons (read more at Phoronix).
The issue is discussed at the Ubuntu wiki, along with some solutions. For me, the fix involved just making X.org use UXA, by including the following in the xorg.conf file, as they recommend in the wiki:
Section "Device" Identifier "Configured Video Device" # ... Option "AccelMethod" "uxa" EndSection