Hi,
I am aware that it helps to put a capacitor across the leads of a motor to help endure its large voltage spike when starting and stopping.
AND running!
How do I know what size capacitor I should be using? For example a motor that runs at 6V, 2 amps stall current.
Newer mind the stall current. If the rotor is locked there will be no commutation sparks and hence no noise (just a really warm fuzzy feeling

).
Find the average (loaded) current (I) and calculate it like this:
The X-cap (the one going from + to - terminal) should be approximately: I^2/10 [µF]
Eg. with a running current of 2A, it would need to be in the region of:
2^2/10 = 4/10 = 0.4µF = 400nF (in which case you could use eg. 390nF).
For the Y-caps (those going from each terminal to the motor housing), use around 1/10 to 1/5 of the X-cap - in the example above, it would mean something in the interval 40nF to 80nF.
They should be soldered directly to the motor terminals and housing with the shortest possible leads (without making life too difficult for yourself) and you should twist the wires going to the motor (and to the battery), so that it has approximately one turn per 4cm to 5cm.
If you have access to a scope, it may be enlightening to scope the noise after each of these remedies are installed.
Just seeing the effect of twisting a lead can be quite an eyeopener
