Some fan controllers have headers for temp sensors. The Aquaero definitely does and it is good....but not cheap. Most of the other Aqua Computer stuff also has temp sensors too though so if any of that is of use, you can plug it in there. Off the top of my head:
PowerAdjust - single voltage controlled header with a temp probe input. If you buy the Ultra version you can control fan speed based on temp. The Standard cannot unless it is plugged into an Aquaero.
Farbwerk - RGB strip light controller but also has temp sensors.
High Flow USB - measure your coolant flow but also has temp sensor input as well as an internal temp sensor (for coolant)
Aqualis XT reservoir - fill level sensor (based on pressure) , internal temp and external temp header.
All these can be run off an internal USB header without needing an Aquaero - or they can team up with an Aquaero of you want....makes it all independent of Windows.