Just for completeness' sake in response to Colin's excellent detailed post:
I have been booting my system with the "iommu=noaperture" setting almost since I installed Ubuntu 7.10 64-bit on my AMD 64x2 dual-core. This was part of solving the "desktop app pause" issues I was having. I was running with an nVidia 6600GT card at the time.
On my PC, in normal linux boot mode it's on, in recovery mode it's left out. I have tried every fglrx that was released since 7.10 and NONE worked on my system (VIA K8t800pro chipset) and video card (ATI HD2600XT AGP 512 MB).
Not that I have a desire to disappoint fred but I am almost certain that "iommu=noaperture" is not the 'magic bullet' for fglrx with Radeon HD2xxx AGP cards
-edit-: yes and I also did try fglrx a couple of times when booted in normal mode with no kernel boot-options included. Just to be sure that iommu wasn't set to noaperture by default when booting in recovery mode.
My full boot-options in "normal" boot are :
ro quiet splash nodmraid notsc noapic nolapic acpi=strict iommu=noaperture