AGND and GND are generally "Analog Ground" and "Everything Else Ground"
The general reason they are separated is that AGND is the reference to sensitive analog circuits (amplifiers, ADCs, DACs, etc...) and GND is the reference for general digital circuits (gates, shift registers, MCUs, CPUs, FPGAs, etc...), which can impart a lot of switching noise onto their grounds.
Now, you want your grounds at the same DC potential so your data converter (just an example) has the same potential analog and digital grounds (analog ground for analog reference, digital ground for communications reference), which is where the CMC (common mode choke) comes in. The CMC has essentially zero resistance at DC (just the DC resistance of the choke), but has a high resistance to AC or frequency components, like switching noise. So by separating your grounds with a CMC you get two grounds at the same DC potential, but you don't get digital switching noise affecting your sensitive analog circuits and/or measurements.
Hope that helped!