From Exploring Arduino Text I am working thru the Exploring Arduino text mostly with success up until chapter 4. I have most of the parts required but for Figure 4-3 I used the following: 

100nF Capacitor, (In place of 1uF Capacitor)

1N4007 Diode Rectifier, (In place of 1N4004 Diode)

S8050 NPN Transistor, (In place of PN2222 NPN)

DC Motor rated for 3V with a Reference Current of 0.35 to .4 Amps (Text lists "DC Motor")

Im aware that the Capacitor was undersized, Diode was a 4 series (so I assumed it was compatible), and the Transistor also the same but of a different manufacturer. Im also aware that the motor is underrated compared to the 9v input, but I didnt think this would cause a problem for a small time period.

My problem is that after about 10 seconds of running (both with the motor free spinning as intended, and sometimes just staying put but making a high pitched noise) the bread board started smoking. So, I disconnected everything and gave up for the day.

What was it that caused the breadboard to start smoking? Do you think I damaged my Arduino?

Link to companion site with diagrams: http://www.exploringarduino.com/content/ch4/
If you used the 9 V battery as described in the diagram, but with a 3 V rated motor, then the motor starts smoking and you might damage it. Use e.g. 2 AA batteries with 1.5 V instead of the 9 V battery, then it should work without smoke and your motor will survive much longer.