For years, we've bemoaned the state of motherboard-based fan speed controls. There are alternatives to letting a motherboard's firmware manage system cooling, though. Fan controllers have been around for years, and Xbit Labs has a good round-up of nine of 'em. The units all come from Lamptron, NZXT, and Scythe, and they cost between $25 and $70. As one might imagine, there's quite a bit of variety in the bunch.
Fan controllers have definitely become smarter over the years, and some of the units in the round-up have automatic, temperature-based speed controls. Brightly lit displays are a staple of most of the fan controllers; some of the screens are large enough to consume two drive bays, and touch functionality has been incorporated into a few of them. If you're looking for something a little more retro, several of the controllers feature simple analog knobs—up to a dozen on one of the units.
The author stops short of picking favorites, but he has done a good job of summarizing the key specifications of each controller, including how many fans it can manage and how much power can be applied to each one. Surprisingly, none of the controllers support four-pin PWM fans. Most case fans still use three-pin DC headers, I suppose.