Software from within Windows, no. If you can find a hardware or firmware solution it's always the preferred option, since you don't want any unnecessary software running. There may be a setting in your BIOS to do it (similar to mine) or you might want to look into a rheobus or something similar for a 3 1/2" bay. If you only want the one fan controlled you don't really need the big ugly rheobus in your 51/4" bay. Alternately, something like this might work for you, by giving you more functionality.
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I wake up in the morning more tired than before I slept
I get through cryin' and I'm sadder than before I wept
I get through thinkin' now, and the thoughts have left my head
I get through speakin' and I can't remember, not a word that I said
- Ben Harper, Show Me A Little Shame
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