thermal control is using intel TM1 or TM2 in the cpu. for when the cpu core gets hot enough it starts to throttle down to lower temps.
Limit cpuid maxval is for older OS's so no issues there with 2000 or newer. as this is meant for Windows 98 and older.
C1E – Intel’s so-called enhanced halt state. Read Anandtech’s blurb about it here for more. Disable initially, enable later on and see if the system remains stable. This is a power savings option.
Execute Disable Bit - enable. XP has a setting to help with virus protection and requires this set to enable.
SpeedStep - Automatically lowers the multiplier from its max. (9x for the Q6600) to 6x when the machine is idle. The result is less power consumption and heat production. It goes back up to 9x when you start to get a CPU load. Disable initially, enable later on and see if the system remains stable. This is a power savings option.
VT,
http://www.intel.com/technology/virtualization/