A couple weeks ago my roommate removed the video card from my desktop to test in his PC. At this time my computer was working fine. After putting it back in, I plugged the power cord in and tried to start it up. At this point it wouldnt start when I pressed the power button, and I saw smoke coming from the case and removed the cord. I assumed there was something wrong with the power supply, and my assumptions were more or less confirmed as the smoke appeared to be coming from there as well as a burning smell.
I did notice however that the little green LED on my motherboard was still on when the power cord was plugged in.

I removed everything and installed it in my roommates case. Upon pressing the power button, the cpu fan would spin for a second and then stop. The green LED is on here as well.

Anyone have any idea what is going on with my desktop? Keep in mind that I tried this with two different PSU's. Thanks a lot.

It sounds like you've blown a couple of capacitors.

Check the motherboard for little battery like things, they should be FLAT on the top, not buldging and they should not be leaking, If they're buldging and/or leaking you've blown a few caps which is pretty unecomomical to fix because there could be other damage and it'd probably mean a new mothaboard.