When we had tried overclocking the NVIDIA GeForce GTX 460 when running Ubuntu 10.04 LTS with the proprietary NVIDIA 256.44 driver and setting the Coolbits option within the xorg.conf we could not get the 2D/3D clock frequency settings to appear. If we were to set the CoolBits value to 5, which is supposed to show both the clock frequencies and GPU fan speed controls, the fan speed settings did appear within the NVIDIA Settings panel but the overclocking options remained non-existent. When popping in non-Fermi hardware the CoolBits options were present.
We have found out from NVIDIA's Andy Ritger that overclocking support is disabled under Linux for all Fermi hardware. Though under Microsoft Windows, the GeForce GTX 460 and other Fermi GPUs can be overclocked -- there's also vendor utilities for Windows like MSI After-Burner and others for enabling clock (core/shader/memory) and voltage controls. Andy says they hope to enable Fermi overclocking support within their Linux driver at some point in the future, but at this point there is no ETA. This is presumably also a current limitation of the near-identical NVIDIA drivers for FreeBSD and Solaris.