Bit of a necro, but I thought it worth adding my experiences in this area.

Having right/middle click switched on GNOME is something that's pushed me to XFCE with Xubuntu for a long time, I want resize on my right button, personal preference, so haing stuck with plain Ubuntu with a 9.10 install, went wandering through the config to set this up.

There is an option in metacity's gconf for "resize_with_right_button", I couldn't get this to work. This turns out that I'm using Compiz and this option doesn't transfer across (unsure whether this is a compiz or GNOME issue). Presumably this will work if you've all effects off though.

Next is ccsm. The instructions from zadehas in post 2 will work, but first you have to untick "Enable integration into the desktop environment" located in "Preferences".
Otherwise you get the behaviour described by vayira where ccsm immediately sets the option back to the GNOME default.

Hope that helps anyone else who comes across this thread with similar problems.