Phillistines! Your poor transition analysis has driven to register on this forum and post my outrage! Clearly the Witches are as follows:
Faye as Granny Weatherwax
Yes, Faye as The Crone. Perhaps the most tenuous of connections, but there are a few things going for this argument. Primarily the disconnect felt by both characters. Particularly in Carpe Jugulum, Granny Weatherwax feels unneeded in the witches' trio. Faye feels somewhat disconnected from her friends at times. Both characters conceal emotional issues. And let's face it, both characters are smart-ass and grumpy.
Raven as Nanny Ogg
Though Raven is the youngest of the Doom Coffee Crew, I think she fits Nanny to a T. First and foremost, both characters are notoriously promiscuous, though Nanny Ogg's promiscuity is a bit more....productive than Raven's. Also, both characters are possessed of a simple, zen optimism about life. And finally, both characters have surprising moments of competence. Midwifing for Nanny Ogg and interior decorating for Raven.
Dora as Queen Magrat
Again, primarily based on Carpe Jugulum (which is one of my favorites), I think that this comparison is apt. Both characters find themselves relatively newly connected (married for Magrat, relationship for Dora) and aren't quite sure about the status of that relationship and where it fits in with their self-image and peer relationships (though Dora has gotten over much of this recently). Also, as Dora is nominally "the boss" and Magrat is nominally "the queen", both characters end up taking orders from the somewhat more bossy Faye/Weatherwax and more convivial Raven/Nanny Ogg.
Penelope as Agnes/Perdita
Eddurd definitely got this one right. Agnes didn't want to be a witch and Penelope didn't want to work at coffee of doom, but both are shanghaied into the job by bossy "elders".
I could also see a minor connection with Mightily Oats as Marten, since in the early QCs (I can't recall which comic precisely) I seem to recall moments of drunken Faye leaning on Marten and making a very similar excuse to Granny "giving Oats permission to lean on her"