How would I measure an Ultracapacitor's Specific Capacitance using a PGSTAT128N?
In the meantime, a method i used a while ago for supercap evaluation. Really simple and effective.

A constant current source (with an ampermeter to make sure it's indeed constant) charges the supercap. In parallel the voltage is measured and a plot is built. With the equation It = CV, C may be determined out of the plot. In the end of charge, a power resistor is used to discharge the supercap.

In my case i had to prove that the supercap capacitance doesn't depend on the charge. Same method works for capacitance measurement. 

For better accuracy select current such that charge time will be long enough, minutes or more. 

Take as many points as you can to filter out any random inaccuracy.