Essentially, in SR4 terms, Potency is a free "Increased Attribute: Magic" power that a GM can give to NPCs. It's a freeby power-up for the NPC in response to meeting certain story objectives. It's also removed from the NPC for the PC meeting certain story objectives.
For instance, take a look at this Guild Wars mission (yes, I know it's Guild Wars and not Shadowrun, but bear with me):
http://gw.gamewikis.org/wiki/Rilohn_Refuge...e_%28Mission%29The party is affected throughout the mission by a certain spell which increases damage from Earth spells by 50%. If PCs complete a set of mission objectives, they can reduce the effect of the spell affecting them. Edit: They reduce the effect by 10% for each objective that they complete. The last objective is very close to the BBEG and if the PCs complete it without drawing his attention, then they can fight him on what is essentially a fair level, with no extra damage from either his spells or the guys near him.
Essentially, when a GM wants to create an "uber boss", a BBEG (Big Bad Evil Guy) whose power is weakened when the PCs don't confront him directly, but rather remove some of the things that gives the BBEG extra power, he gives the boss additional Potency. In my opinion, it doesn't exist in SR4, because there doesn't need to be a special mechanic for simply giving a BBEG more dice to roll unless the PCs have completed certain objectives (or giving him more dice to roll if the PCs fail to complete certain objectives).