I have 2 extra very fast fans (I dont know exact RPM though) which I can put anywhere inside my cabinet. The problem is that I cant figure out where to put them exactly so that it will cool my processor properly.
Here is my config and temp on which it currently remains when idle (I opened my cabinet to keep it cool and clean it regularly)-

Intel core 2 duo E6600 (2.4GHz, 4MB L2 cache, 1066FSB)- 45-47C (already contains a heat sink and fan)

Nvidia Geforce 8800GTS 640MB graphics card- 63C at 50% fan speed of its own fan and 54C if 100% fan speed.

Other than its own fan, this graphics card has a big aluminum heat sink too, so I am not worried about its temp.

2GB 667MHz RAM.

320GB 7200RPM HDD + 250GB 7200RPM HDD- both 40C

Sound blaster 5.1 Live sound card (this is not so hot)

500Watt PSU- contains a fan.

intel 946GZ Mobo.

so there are 3 fans working and one heat sink. Now I have two extra fans and my whole box is open so I can put them anywhere.

Note:- The mobo is vertical on cabinet wall (as usual) and GPU is perpendicularly attached to it (as usual). The GPU is very big and fan is very lite so I can put it on GPU too. That makes fan exactly in front of mobo. Now I dont know whether to put fan in front of heat sink of mobo or directly in front of fan which is attached on processor, or anywhere else. Please tell me which position will cool processor more (or any other position in cabinet).

One fan I can put right below the fan of GPU so that it blows the hot air out, which comes out of Graphics card. Is it all right or I should try some other positions.

I have explained all positions of my hardwares. please help me to use those two fans efficiently.

Hi, is this a recent build? If it is did you apply the grease between the cpu and the heat sink? Are the temps you posted at idle? And is this the heat sink and fan that came with the processor? Instead of trying to add more fans to your case, you may want to check into getting a bit larger CPU heat sink and fan or even water cooler for it. Newegg.com has these items and at good prices. If this is a new build you may have to let it "burn in" for a few days and then see if the temp don't even out. You said tthat this is an Intel mobo, did you get a utilities disc with it? If so you have a program on it to momitor the temp on the board. It is a cool little program and it will show you the red zones for certain areas on the board. If you don't have the disc go to the Intel site and search for it under desktop utilities.

Personally I wouldn't say there is much point in water cooling unless you are going to overclock. I can see from that spec your a gamer/3d designer, unless you wouldn't have spent £300 on a GFX card.
You need to make sure fresh cool air gets to the cpu fan. Eg. An intake fan blasting at the CPU from the side of the case. You don't need that much thermal paste, but with a dual/quad core you should run a small thin line across the CPU/heatsink. dont go overboard. Sigle core CPU's should be a small dollop in the middle.

Not sure about images in these forums, so if this doesn't appear use the link below to see what I've done.

The intake fan in the top left is now in the side of the case feeding air directly above the CPU.

I'm running a Core2Quad Q6600, on an ASUS P5K Mobo, with a lowly nVidia 6800, and I have been getting temps of 27°C (motherboard) & 32°C (CPU) when Idling, 31°C (mobo) & 42°C(Max) under heavy load. This is using stock CPU heatsink and fan, and in summer, but I suggest paying out for a decent fan/heatsink combo. Somthing like this: http://www.scan.co.uk/Products/ProductInfo.asp?WebProductID=500678 as it can be positioned to direct heat directly towards an exhaust fan, and has good dissipation.
You could also benefit from some Arctic Silver heatpaste if you think intel are a little stingy on the amount they dish out. You'll probably want to have an equal intake/exhaust fan combo, but If like me you have a dual fan PSU you'll prob want an extra intake as you could get overheating probs.

Another thing that helps, is good cabling. You'll need good circulation, and theres no point having dusty fans that are blocked by things which render it useless