Using output pins to heat up CycloneIII

I think achieving a constant Tj temperature using a heat generator design will be difficult if you want any other temp besides whatever it hits when it reaches steady state. Some thermal chambers will let you put a probe on the device and it'll monitor it and try to keep the temperature as constant as possible.

A pelt like dwh suggested might work well too if you get the voltage right. You'll want to get a thermal probe in between it and the device since if you don't figure out the thermal resistance ahead of time you might be surprised with the temperature you end up with. Don't let the name 'cooler' throw you off, they can cause a chip to get very hot under the right conditions (or wrong conditions if you wanted to cool the part :)).