3V motor and some kind of single-chip PWM + speed control part would be great. If you can fit it in your budget, TI has some low-cost, low-current single-chip motor controllers IIRC, that do the PWM, back-EMF readout (including readout of measured speed via SPI, I believe), and even bells and whistles like motor speed ramping.

Next choice, 3V motor, PWM for speed control, and back-EMF

That is unless your device has a boost convertor already used for something else, and you have an underutilized 6V / 9V rail with power to spare :-)