I'm happy to report that the subject is mostly fixed.
Window List: bgo#86382 has a working patch, it's not perfect (read comments 140, 141 and 145) but fixes the problem.
Notification Area: bgo#531371 also has a patch which works really well.
Quick Launch: My fix is included in version 2.12.6 of the applet.
Main Menu: The ugly arrow (bgo#562247 and bgo#564903) can be removed by setting
FALSE in gnome-panel/panel-menu-button.c
Keyboard Indicator: bgo#591515 is not yet fixed. A quick and dirty hack is to comment out the entire switch statement in
GSwitchitAppletUpdateAngle() function from gswitchit/gswitchit-applet.c
I'm using a GNOME desktop with all these fixes daily and I'm quite happy with it. You can get my customizepkg files for Arch Linux from GitHub; read how to use them in the previous post.