I was having the same problems you were with the PC fan based stir plates. I was having trouble with the magnets I had saturating the hall effect sensor used in the brushless motor; Im guessing my magnets are just overkill (1"x0.25" round N42 Neodymium...big motherf***ers). I also had stability problems with the 2" stir bar for my 2000mL Erlenmeyer flask.
So I busted out my lathe and turned a disk to hold the magnets and paired this disk with a 12V (60mA) 1200RPM gear motor. I had to dick around with the gears to get the reduction I wanted (originally a 300RPM) but it works now. Mounted the thing in a 4" PVC coupler and used some 1/4" Plexiglas for the top base. I have a PWM motor control I built (still on breadboard...) to vary the speed. Only problem is the gear noise from the motor is loud...not too bad when the shit is in the fridge but if its sitting out its loud. If anyone wants some pics I can post them.
EDIT: Opps...Hit the wrong button and this was supposed to be in the stirplate thread...I'm a fucking idiot...