The E6400 sounds like a great selection to overclock using option #2 for those of use who are tight with the bucks, but is possible to "On the Fly" slow everthing down, so to enjoy the best of both worlds.
1.) a fast cheap system to use when performance is desired
2.) a quiet system to use for everyday tasks such as email, and surfing
Many motherboard manufactures have Windows based overclocking utilities the will allow you to overclock on the fly from within windows (i know gigabyte calls theirs Easytune). I dont know if any of these do it automatically though. You could also use RM Clock to adjust the multiplier and throttleing on demand, providing Core 2 Duo provides the same power management options as the mobile Core Duo.
Maybe overclock from the BIOS to what your max will be and then slow it down using RM clock once your in windows.
Im a little behind on the latest desktop overclocking and power mangement though so look into it more. I only know about RM Clock cuz i use it on my laptop, which is a Core Duo T2500
The newer Asus boards have AI Gear. It's a "gear shifter" that you can move from 'Performance' (high clock, fans on full blast) to 'Silent' (throttled down CPU, fans all quiet) without rebooting. Also, a program called SpeedFan might do what you are looking for.
Asus had what i wanted in terms of overclocking/Noise Profiles in the P5W DH Motherboard.
I can overclock my little 6400 to 3.0ghz. and at nights i just click the remote control Zero Noise profile and with CPU power savings futures from intel the fans slow down enough from not being a pain to my ears.