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.
Walternate - Unholy fusion between Complete Monster and Magnificent Bastard with a touch of Omnicidal Maniac for spice; or simply a man who saw a series of attacks on his entire universe - that have killed thousands, if not millions, starting with the kidnapping of his son, and may possibly culminate with a Class X-4 Apocalypse - and believes this to be the result of a deliberate attack by "our" side, and thus regards himself as fighting a war. John Noble sees it as both.
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.
Complete Monster: Evil Brandon suggests killing Olivia pretty much for the hell of it.
Cop Out: The whole thing with Mr. X feels like the biggest cop out ever. Not to mention, NONE of it was even remotely clarified within the show - Wyman had to get on Twitter to tell us the connection.
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.
Fan Preferred Couple: Most everyone would love to see Lincoln (alternate universe) and Fauxlivia together.
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.
After the episode "Peter", the series generally lost its monster of the week formula and the alternate universe angle became much more prominent. The show has been far better ever since.
There's a lot of first season contenders for which episode Grew the Beard, all of them being episodes that introduced some element of the Myth Arc.
"The Arrival", which introduced the Observer.
"In Which We Meet Mr. Jones", which gave us the first Big Bad of the series.
"Ability", which fleshed out ZFT and the concept of the War with the Other Side, and introduced Olivia's cortexiphan abilities.
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.
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.
It's okay to squirm during scenes like Flight 627, the shades-of-Alien pregnancy scene, or when people's skin start growing over their eyes...and ears...and mouth...and other places. Really.
Toy Ship: Young Peter and Young Olivia in "Subject 13".
Uncanny Valley: The Observers. They're pale and hairless, speak in a Creepy Monotone and have an odd way of staring at people. They're more in the "off-putting" rather than "scary" part of the Valley.
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.
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. She spends the whole third season premiere alone in the alternate world, desperately trying to get home, only to have her hopes crushed at every turn. She tries to resist Walternate's brainwashing, even when it means rejecting the comfort of her alternate's mother (who has been dead years in Olivia's world), only to tearfully break down and succumb. After escaping a horrific death by the skin of her teeth, she finally gets home... and then realises what Peter and Fauxlivia were doing. 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.