Nope, there are programs that can MONITOR them, but I haven't heard of any program that can actually lower the voltages delivered to your fans by software.
Speedfan (I use it to monitor my CPU/GPU ect. temp) has options to do it, but strangely I just went to verify it, and it freezes when I get there... my computer never freezes.
I'm fairly sure you can't through software, but I could've sworn I saw it.
I don't really mind it when I'm on it, but I'd like to leave it on while I sleep, and the humm from my current fans are just annnoying the fuck out of me.
I've done a bit of research, but it seems I need to find the right fan for my MOBO I'm planning on (neo2 platinum) some huge ones just don't fit on it.