For CPU processing, unless you already use an upgrade I'm unaware of any overclocking software; all the overclocking I've done has been hardware (dip switches, soldering, that sort of thing). I know that you can mess with the speeds of earlier Sonnet upgrades using their plug-ins, but I don't suggest trying them with a stock processor (if they'd even work).
If you have an ATI graphics card, you can overclock it on the fly with ATIcelerator II. For Nvidia, you'll have to mod the ROM and flash it.
As far as I know, you can't overclock RAM, and you can only overclock the bus on certain computers (and it almost always requires micro-soldering).