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Yeah, it would be pretty hard to write a program that controlled the fan connectors as they vary by motherboard. Your best bet would be an internal serial connector on the motherboard as oberon suggested. Either use a switching transistor or a relay and some simple com commands. You could then power the smoke generator by a spare molex connector.
The com commands can be done easily enough with C++ or VB, so the only real problem would be fabricating the smoke generator.
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"Empirically observed covariation is a necessary but not sufficient condition for causality" - Edward Tufte
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