Hi Keld,
with a long shaft like that supported in a single bearing, it will need dynamic, not static balancing - imagine you have two 500g weights on the shaft, equal distances from the axis of rotation, that balance each other when it's not rotating - it will appear in balance, no problem and at very low speeds there won't be much vibration. This is static balance, and you should aim for this before thinking about dynamic balance! Now consider a 490g weight opposite each of the 500g weights - the shaft will still be statically balanced.
Now, if one pair of weights is 10cm up the shaft, the other 20cm, when the shaft spins the imbalance in the weights 20cm along the shaft will put twice the torque into bending the shaft, and both the ends of the shaft will try to move in circles - 180 degrees out of phase (assuming the fixed end isn't *completely* rigid and attached to something the weight of the universe!).
SO... what's needed is counterbalancing weights to make up for the imbalanced weights - but how to find where to put them?
In a lab, you could use a strobe lamp synchronised to the shaft rotation - this would let you see a "snapshot" of the shaft bending so you could compensate with balance weights / drilling the heavy spots.
In the workshop, you could put a compliant bush (e.g. hard rubber) around the bearing, and use some kind of marker (a brush and layout blue, a whiteboard pen?) to mark the high (therefore heavy) spot as it comes round - the rubber bush would allow the heavy spot to deflect outwards and touch the marker. This would leave the need to mark the other end though - once the "free" end was balanced, you would have to mark and balance the bearing end, then repeat the process taking each end in turn as you got closer and closer to dynamic balance...
Tyre balancing machines work sort of this way, but often they put the compliance in line with the wheel centre, which makes it obvious which side of the wheel needs additional weight, as well as where on the circumference.
Luckily, motorcycle wheels aren't wide enough for weight distribution across the width to make much difference

Take a look at
http://en.wikipedia.org/wiki/Balancing_machine and
http://www.precibalance.com/gfaq.pdf for a bit of info, expressed far more clearly than I can!
Dave H. (the other one)