How to choose reference current in a charge pump circuit?
The reference current IREF will set the amount of charge delivered/extracted to the output in each comparison cycle. How much is needed depends on the application where the charge pump is used. For example in PLL circuit this current together with VCO gain, resistor and capacitors connected to Vcont node (as shown in your example) will set loop dynamics. That is bandwidth, stability margins etc. So IREF current is one of design variables that you should choose while designing your control loop (ie. circuit using charge pump).

As to how it can be physically implemented, there are a lot of possibilities. Simple one being just resistor - if you can afford big variation and poor power supply rejection, more complicated could be some kind of bandgap circuit for steady voltage reference together with voltage to current converter.