top fan should ALWAYS be exhaust (remember, hot air rises), back is usually exhaust (ATX standard), front should be intake (because the cold air will be on the floor) and the side fan (if you've got one) can be either, depending on what card you've got (for single slot coolers it should be exhaust, for dual it should be intake)
i always use CoreTemp 0.99.3, because it reads the actual temperature diode within the CPU, not the thermistor located below the socket... 51C is quite hot if you're running stock... make sure you haven't got too much thermal paste between the CPU and heatsink (because this stuff is really not that conductive... compared to the sink)... also you could consider lapping the sink and the CPU itself to help with conductive cooling