I'd use whatever heatsink came with the processor - I'm sure lots of engineering went into making sure it was a good match.
Here's a side-by-side comparison of both processors:
You are right, the newer processor uses newer technology (45nm vs the older 65 nm) which allows packing more transistors into a smaller die and consumes less power (95W vs 105W for older), interestingly the case temperature is qualified to run hotter (71.4°C for newer vs 62.2°C for older). So the newer processor has a lower thermal design power (http://en.wikipedia.org/wiki/Thermal_design_power) *and* is qualified to run hotter, therefore a smaller heatsink/fan will do the job.
Name Intel® Core™2 Quad Processor Q9650 (12M Cache, 3.00 GHz, 1333 MHz FSB) Intel® Core™2 Quad Processor Q6600 (8M Cache, 2.40 GHz, 1066 MHz FSB) Code Name Yorkfield Kentsfield Status Launched Launched Launch Date Q3'08 Q1'07 Processor Number Q9650 Q6600 # of Cores 4 4 # of Threads 4 4 Clock Speed 3 GHz 2.4 GHz Cache 12 MB L2 Cache 8 MB L2 Cache Bus/Core Ratio 9.0 Bus Type FSB FSB System Bus 1333 MHz 1066 MHz FSB Parity No No Instruction Set 64-bit 64-bit Embedded No No Supplemental SKU No No Lithography 45 nm 65 nm Max TDP 95 W 105 W VID Voltage Range 0.8500V - 1.3625V 0.85V-1.5V 1ku Bulk Budgetary Price $316.00 $183.00 Package Specifications TCASE 71.4°C 62.2°C Package Size 37.5mm x 37.5mm 37.5mm x 37.5mm Lithography 45 nm 65 nm Processing Die Size 214 mm2 286 mm2 # of Processing Die Transistors 820 million 582 million Sockets Supported LGA775 LGA775