Core 2 Duo does not get that hot, unless you overclock the crap out of it. It's not surprising that a CPU that's overclocked 50% runs around 60C (An E6600 running at 3.6GHz for example). Plus, if you strike luck with a 'B' version of a good week, temperatures are better.
A suggestion for a rig:
CPU: Intel Core 2 Duo E6600 Conroe 2.4GHz $309.00
MoBo: ASUS P5N32-E SLI Socket T (LGA 775) NVIDIA nForce 680i SLI $299.99
RAM: Crucial Ballistix 2GB (2 x 1GB) DDR2 1000 (PC2 8000) $309.99
Video: eVGA 768-P2-N831-AR GeForce 8800GTX 768MB GDDR3 $599.99
HDD: Western Digital Caviar SE16 WD2500KS 250GB $79.99
DVD: LITE-ON 18X DVD±R Burner Black IDE $29.99
CPU Cooler: Scythe SCINF-1000 120mm $57.99
Case: COOLER MASTER Centurion 5 CAC-T05-WW Black/Silver Aluminum Bezel $49.99
PSU: SILVERSTONE ST85ZF ATX12V/ EPS12V 850W $279.99
Maybe it's possible to find a case that leaves some space between the bottom of the motherboard and the bottom of the case?