I have found this very unusual that while running Windows OS my Thinkpad T400 is extremely silent and smooth but while running linux OS like Ubuntu( tried 386 and 64 bit ) , mandriva , centos . My T400 runs much warmer and is difficult to use this way.
While CPU usage may be reported low at idle, power management drivers may not be optimized and properly scaling CPU and GPU cycles. Switchable graphics models operating in discrete mode may generate more heat and exhibit reduced run time due to the higher energy consumption.
Recomendations: Install most recent kernel / release for the distro being used and consider installing and powertop.
For switchable Intel / ATI models, try going into you BIOS and change the switchable graphic option (or discrete graphics) to integrated graphics. Running on integrated mode will reduce power consumption and lower the thermal profile of the system.