After Gnome has been running for about a week, I notice that certain window operations, in particular changing window focus and closing windows, slow down. This seems to be particularly pronounced when closing windows. The contents of the window is blacked out and remains that way for up to a couple of seconds before it disappears. While it is in this state, the mouse is frozen. This makes it inconvenient to close many windows in succession. The slowdown is cumulative over time, or possibly with use; the longer the session is up, the slower it gets. I have not noticed this with KDE. I always run Gnome with Enlightenment and KDE with the KDE window manager, so I don't know if the problem is in Gnome, Enlightenment, or a combination of the two.
I have found that when window operations slow down, restarting the Gnome panel (that is, killing it from the shell and allowing it to restart itself) restores the performance I see just after starting the session. I have upgraded to Enlightenment 0.16.4 and am using its pager and iconbox features to replace the Gnome pager and window list. I have turned off these features in the panel, and have not seen a problem with window slowdown since.
A new GNOME release is coming out soon which includes many fixes and updates to the Panel... including the GNOME Pager which has been replaced with the Desk Guide... this applet has been a source of many issues of this nature. We will see if the new release fixes these issues - which in the initial review seems likely.