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Using `modprobe -r agpgart fglrx intel_agp` should do what you want (you may have to change the order or some other modules as well) until you reboot the system.
To stop them loading on a reboot try grepping your startup scripts for the modprobe command or for those module names. Have a look in /etc/modules.conf in case there are references to them there...
You could just recompile your kernel and remove support for agp - are you sure you don't need it?
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