Had a heck of a time dealing with stepper induced vibration. It confuses the tilt sensors making it difficult to balance the 6-foot tall robot. Aside from microstepping and using sinusoidal current control, not sure what more can be done aside from filtering the accel & gyro measurements. I think it worked out okay, but if there's more that can be done, I can use the tip.
https://www.youtube.com/watch?v=Xmt67HTI2Hg
I used the ST-M5045 stepper drivers found at Sainsmart. Stepper are KL23H276-28-4B dual-shaft 2.8A motors.