i agree that pop up window is nice siphon recovery but its a double edged sword. if the runner was paying 1 credit and a click for a 20 percent of winning 5 credits they probably would be right to be running every time. the runner in reality is paying 1 credit and a click for a 20 percent chance of winning over 1/3 of the corps "stack" of losable agenda points. while i dont think you can determine an exact click or credit value for an agenda point i think the poker concept of pot odds is applicable.
First of all, the thing about popup window is that its usually not: "Popup window versus (other ice)". Its: Popup window versus not being able to rez any other ice. So its massively better for you to get $1 and the runner to lose $1, than for them to get in completely free.
Second, the money you get from multiple popup runs by the runner, accessing 1 card at a time, pays for you to put another ice there and rez it. It helps you build the real defense.
Third, popup is extremely efficient. $1 for the corp is actually more valuable than $1 for the runner, since runner economy is so much stronger. Therefore, the result of popup (without Yog) is worth more than a $2 swing.
If you have a Wall of Static, it ends the run. But as soon as they get Corroder, they are breaking your $3 cost ice for $2. Popup still results in a better than $2 swing, and it cost $0!
If you have an Enigma, it ends the run and they lose a click. But as soon as they get Yog, they are breaking your $3 cost ice for $0. Popup still gives a better than $1 benefit, and it cost $0!
On average, five runs on that R&D will result in the runner losing 5 clicks, $5, and you getting $5, and they will average 2 points. I would generally spot the runner 2 points to get that kind of early advantage. (I'm not going to want to keep doing it once they have points of course). And of course, if the runner is doing anything more than accessing 1 card, the situation gets much worse and DEMANDS additional defense. For example, if the runner has R&D interface and Desperado, you need more ice there asap.