These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Played with in Season 3: Walter says he no longer sees Walternate as pure evil after facing the choice to seal a soft-spot with amber. Walternate, in turn, says he will never authorise experiments on children, a line Walter crossed a long time ago. In Season 4, with the alternate timeline, Walternate is no longer a bad guy, but remains mistrusted by "our" side.
David Esterbrook from The Cure. He's a pharmaceutical executive running a program turning young women suffering from a rare disease into radiation-emitting bioweapons and tested it out on a cafe of innocent people.
Morgan Steig, from the pilot episode. He releases a flesh-melting toxin aboard a crowded airplane as a demonstration to potential buyers; worse still, the toxin arrived on the airplane through the insulin pen of his unsuspecting twin brother, who was chosen as a victim simply to show just how dedicated Steig was.
The unreformed Nazi in "The Bishop Revival" who develops a toxin specifically to target and kill Holocaust survivors and their descendants is one notable exception. He tests his toxin on a bunch of random people in a coffee shop just to see if it'll kill everyone with the genetic traits that he picked and in the end tries to disrupt an international peace conference with a massacre just for the hell of it.
Wyatt Toomy and Reverend Marcus from "The Abducted" absolutely qualify too. They abduct children, steal youth from children to keep themselves young, leaving the kids permanently disabled.
Despite being an absolute complete dick, a lot of fans have taken to Windmark.
Ensemble Darkhorse: Charlie, Lincoln (in both universes), Gene the cow , Scarlie, William Bell, Brandon, Sam Weiss, Henry Higgins the cab driver, and Asteroid! Er... I mean Astrix! Oh wait no. Astro! That's it.
At the beginning of "Concentrate and Ask Again", a guy comments that he never wants to hear his friends sing again after they sing "Happy Birthday" for him. Yeah... he doesn't last past the opening theme.
A lot of people like to think Broyles' stint in "Lysergic Acid Diethylamide" was one big Crowning Moment of Funny. That is, until he starts "seeing death" - starts seeing himself. Seeing his alternate self's mutilated corpse at the end of "Entrada" scared and scarred him more than he'd ever admit.
Watching "Unleashed" (S1-E16) after "A New Day In The Old Town" (S2-E01): the episode is about trying to save Agent Charlie Francis from being killed by the larvae of a hybrid monster inside him. It also shows his family. Then, in A New Day in The Old Town, the writers Dropped A Shapeshifting Assassin On Him.
William Bell warning Olivia about how terrible and horrifying the Shapeshifters are becomes a little bit unsettling when we find out Bell invented the damn things.
Walter/Bell. Walter even has an affectionate nickname for "Belly." In 3.20, Walter tells Bell that he needs him. Now imagine that whole conversation between a man and a woman who've known each other for a long time...
"We could have been so happy together." It's like they forgot to be subtle about it.
Lincoln (the one from the original universe) with both Peter and his late partner Robert Danzig.
There is a chemical that causes your orifices to seal themselves shut. It's most commonly distributed on plain 'ol American paper currency. If some attempts to trach-tube you, your skin could simply grow over the trach. A two-dollar bill to be exact. Though Walter posits that they were just "showing off"; there's nothing to stop them from putting it on any given bill. Say, you got change for a twenty?
Right now, people from another universe could be watching you. And you'd never know it.
A shape-shifting assassin may have killed and replaced someone you know. Maybe a co-worker, maybe a friend, maybe a loved one. They look the same, act the same, and even have all the same memories. By the time you realize something's wrong, it's probably too late.
"No Brainer" gives someone melting brains using the internet. Now if that's not high octane paranoia fuel to everyone reading this page, you must have a fantastic popup blocker.
Seasonal Rot: Not as pronounced as in a lot of cases but for some people the switch to an alternate timeline and the confusion as to whether we should see these characters as the those we knew for the first three years or merely alternate versions caused problems and emotional distance from the storyline.
She Really Can Act: Many viewers who were underwhelmed by Anna Torv's performance changed their minds at the end of Season 2, when they saw just how convincingly she could play Olivia and Fauxlivia as two separate characters.
Nina and Broyles. They kiss in Season 2. This is never brought up again.
It was suggested that Nina had a thing for William Bell throughout the series. Considering he tried to use her adopted daughter to destroy the two universes and made no attempt to save her life, the ship has probably sunk.
Pretty much everyone for not noticing that Fauxlivia was acting odd. After a mission to an alternate universe. Where they know there is an alternate version of her. Also shapeshifters who can look like anyone. Not a single red flag.
Similarly, no one checking to make sure Charlie... was Charlie after he was replaced by a shapeshifter. When they knew they were fighting a shapeshifter. Seriously, guys...
More a case of Grief Makes You A Dumbass, but there is not a chance that Peter inserting Observer tech into his brain without knowing a thing about it is a good idea.
As much as Walter deserved to be locked away for his experiments in the past, one can't help but feel for him when he starts crying or suffers a Heroic BSOD as a result of his inability to deal with the skeletons in his closet.
Peter in season 4 and 5.First, no one remembers that he existed. Then he loses his three year old daughter. Then she dies.
A lot of the minor characters come to mind. Christopher Broyles and Joseph Meagar just to name a few.
Rachel Dunham, Olivia's sister. Her husband is a jackass.
Olivia. In Season 1, her boyfriend dies (but not before she finds out he's a traitor), she gets kidnapped and discovers that she was experimented on a child. In Season 2, she crashes through a windshield, develops PTSD, falls in love with Peter, Peter leaves, she goes to rescue him from an Alternate Universe, she gets left behind in said Alternate Universe with no obvious way of escaping and Walternate tortures and experiments on her. In Season 3, she gets mind raped into thinking she's her alternate self, she remembers who she is, she gets captured again, she gets rescued and comes home only to discover that Peter was doing her alternate. In Season 4, she can't remember the love of her life even existed, she's being drugged against her will so that she can be used to power some doomsday device, she remembers the love of her life but forgets her surrogate mother, and then she gets shot in the head. At some point between 4 and 5, her daughter goes missing, her world is invaded and she and Peter have a falling out. In Season 5, she spends 20 years in amber and then bonds with her long lost daughter, who is then unceremoniously killed off. She then finds her surrogate mother after Nina is forced to shoot herself in the head. Young Olivia was even more Woobie-ish. After Walter frightens her into blowing up a room, she runs away. Not because she doesn't want to be experimented on any more... but because she thinks that she "messed up" and that Walter will send her away. That's right folks. She's so terrified of her stepfather that she'd rather be in an illegal drug trial. Seriously... just look at her.
Amber Timeline Nina Sharp, considering her daughter can't remember her, her granddaughter died, she's in love with an Omnicidal Maniac who screwed her over epicly, she spends 21 years without her family, in a wheelchair with a broken cybernetic arm and surrounded by mind reading invaders from another time, she thinks that the only thing she's good for is helping the Fringe team, and when it gets out she's part of the resistance she's forced to perform a Heroic Suicide to stop herself from betraying Olivia and the others. Her life sucked.
If Fauxlivia wasn't upgraded to Jerkass Woobie status at the end of Season 3, she definitely was when Lincoln gets shot.
September AKA Donald. He's basically been alone for 21 years but not after being experimented on and banished by the other Observers.
And a case of fridge horror, can you imagine what it must have felt like, for September to get up, and suddenly be hit with raves of emotions? And also to live must of his life as Observer and to suddenly have all that taken away?