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.
Big Lipped Alligator Moment: The end of "Funhouse", which, instead of ending on Cal and Emily and the burned birthday cake, gives us a mouse's-eye-view tour of the Lightman Group, ending by finding the mousetrap Cal set at the beginning of the episode.
Andrew Jenkins from season 1's "Blinded" is a Serial Rapist whose crime spree involved raping 12 women. When he was done, Jenkins would focus their gaze on him before he blinded them so he would be the last thing they ever saw. Knowing a copycat of his is out there and kidnapping a woman to blind and rape, Jenkins enjoys playing a twisted game with hero Cal Lightman as Lightman tries to save the woman. With a reach extending outside prison, Jenkins has a guard pass letters to his copycat by threatening the man's daughters and promises Lightman his copycat's next victim will be someone Lightman loves.
From the same episode comes Jenkins's copycat, Paul Russell, who is also a Serial Rapist who collaborates with Jenkins to gain as many rape victims as possible. Not content with just raping and blinding women, he married one of his victims later so he could always be close to one of his "masterpieces."
Martin Walker from season 2's "Beat The Devil" is a Serial Killer and torturer. At first, he gains Lightman's notice when he becomes aroused by seeing photos of women being tortured. It comes out Walker is a vicious murderer who gets his kicks by waterboarding young women. He then forces them to dig their own graves before murdering and burying them in them. The waterboarding is related to how he allowed his sister to drown as a child, allowing her to drown merely because he wanted her bike.
Dude, Not Funny!: Cal snarking around in the crazy house and mentioning he has "an intimate connection" to suicide, especially when you remember "Depraved Heart", what happened to his mother, and the fact that 30 years later, he still blames himself for it.
Growing the Beard: Most critics seem to agree that the storytelling got much more dynamic with the inclusion of ShawnRyan as co-Executive Producer in the second season.
Harsher in Hindsight: The plot of 'Undercover', which is eerily similar to the Trayvon Martin tragedy... which happened three years later.
Ho Yay: Cal and Jeffrey, his buddy from Oxford in one episode.
And Cal comes onto the character played by David Anders, but that's just to get a rise out of him (it doesn't really work).
Let's face it, Cal/every male character. His complete lack of respect for personal space just amps it up.
Jerkass Woobie: When Cal finally opens up and admits his failings and feelings, you just want to hug him. A particularly poignant example is the opening sentences to his (as yet still-unwritten) book:
"Let me be clear. I understand very little, least of all the people closest to me."
Special Effect Failure: In "Love Always", Cal demonstrates the shocking effects of gunfire by firing a semi-automatic handgun in the air; the scene is repeated in slow motion, too, and the gun is visibly fake: the slide doesn't move, and no bullet casings come out.