I remember a security guard near the finale, but that's about it. Was it more common than my memory tells? What does that say about how little it impacted upon me?
The main scene I remember where one of the protagonists resorts to torture is in the final season where Peter tortures a captured Observer to figure out how to put together a time portal stabilizer the Observers are using for transport. But if I remember the scene correctly, Peter doesn't even want information - he's just really pissed off at the Observers for killing his daughter. Even though this scene shows one of the protagonists doing something wrong, I question whether it was really trying to get the watcher's approval for the his actions. If anything, it was trying to show disapproval for his actions by depicting him as mentally unstable. I'm not saying that there aren't more scenes where the protagonists resort to torture, just that I can't remember them.
A further question that I have is what exactly torture is in a sci-fi show. There are at least two episodes where the Fringe gang uses a device that reanimates a recently deceased enemy so they can get the necessary information to stop an impending attack. Is a scenario like this torture? And what about when one of the Observers attempts to read Walter's mind causing him a great deal of pain? This seems to be torture, but would the shows viewers think that governments should torture because Fringe depicted a character reading another character's mind?
Finally, Ntrails makes a fantastic point. Typically, torture is not depicted as a critical story piece in Fringe. Torture occasionally makes appearances, but many of the shows fans can't even remember when and how often they were used. What does that say about the "legitimizing" force of depiction of torture in Fringe?
Anyway:
http://en.wikipedia.org/wiki/The_Same_Old_Story - Victims are paralysed with a muscle relaxant and then have their faces peeled off.
http://en.wikipedia.org/wiki/The_Arrival_(Fringe) - Multiple victims are strapped to tables and tortured. Three scenes in all I believe.
http://en.wikipedia.org/wiki/The_Cure_(Fringe) - Woman strapped to a table, she's a test patient being tortured with painful drugs, begging them to stop.
http://en.wikipedia.org/wiki/Bound_(Fringe) - Olivia strapped to a table and tortured.
http://en.wikipedia.org/wiki/Inner_Child_(Fringe) - Woman are paralysed and then slowly killed.
Well that's the first season. I'm off for dinner now. If you want to try something similar for the first season of the X-Files please do!
(Sorry couldn't reply to your reply, I think it's too deeply nested or something)
Fringe, especially in its earlier "monster of the week" seasons, has a very clear distinction between the "good guys" and the "bad guys". Since only the bad guys are committing torture, it seems more plausible that the writers of Fringe think that the audience will view torture as something bad people do. However, it does not support your point that torture is a tool used by everyone.
There's one plot line in season 5 where Peter tortures an Observer. But it was depicted as a moral failing of Peter to commit torture, opposite what you suggest in your OP ("In fact it’s often portrayed as a moral failing to not do anything it takes to get the results you need.").
The entire plot line is very dark as Peter's grief over his daughter takes him down a bad path. It is supposed to be (and was for me) uncomfortable to watch.
In your article you specifically state, "Torture is used by all parties. Everyone resorts to torture, whether they are the good guys or the bad guys."
You then use X-Files and Fringe as the main points of contrast. This is blatantly wrong. All of the examples you have pointed out above, as well as all of the instances of torture I recall from the show, were from the "bad guys".
I would disagree with this being a form of normalization of torture, but rather a statement against torture. The bad guys use torture because they are bad; ergo this is a quiet form of protest from the shows producers against things going on today; Guantanamo, water boarding, etc...
The final act, him cutting open and killing the observer is still shocking, and it isn't glorified or seen as right. It's clearly the first steps down a darker path.