RGB Led strip pot control burned my arduino?
First, as Majenko said, you need resistors between the arduino output pins and the transistor bases. Start at something like 330 Ohm.
Second, what is the value of the potentiometers? If it is too low you would be drawing too much current from the 5V pin to the ground.
Third, you should power the arduino with at least 7V, assuming you power it through the Vin pin or the power jack. 6V is considered too low.
I assume the pins connected to the potentiometers are initialised as inputs. Otherwise, it would be possible to burn your arduino by having them source/sink too much current (i.e. by turning the potentiometers to one end or the other).