My build is now complete. As it runs, I can faintly hear a sort of howl-ish sound coming from the case. I can't figure out which of the fans is doing it, but its a bit annoying nonetheless.
The fans (They're blue LED fans) are also much brighter about 2 seconds or so after I hit the power button than they are during normal operation. Thats not anything to worry about, is it?
If those fans are connected to the motherboard and controlled through that they're probably just running at full throttle until the fan controller on the board is booted and functioning. Check your PSU, they sometimes can make weird sounds too. It's probably a fan though.
I'm now fairly certain that the noise is coming from the CPU cooler, as I used SpeedFan to disable all the other fans. After disabling the cooler (or at least letting it as low as the program would let me), the noise went away. Should I return the CPU cooler? I've had it less than 30 days.
None of the other fans in my case, no matter how big or small or for what purpose or speed setting, make any similar noises to this one.