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.
Alternative Character Interpretation: Is the Man From Another place legitimately trying to stop BOB to prevent a catastrophe from happening, or is he an evil spirit trying to take control of BOB for his own purposes? Due to the show's cancellation, we may never know for sure.
His motivations remain mysterious in the show, but Fire Walk With Me lends a darker interpretation to his character. He seems opposed to BOB only in that BOB hoards garmonbozia for himself and deprives the other Lodge creatures of their rightful fill. The Man From Another Place is happy to slurp up the garmonbozia that BOB proffers after killing Laura and thereby inflicting suffering upon both Laura and Leland.
Further related to Fire Walk With Me, he claims to be "the arm," (likely) meaning Mike's arm - a remnant of Mike's own evil. I've always thought that the Black Lodge denizens were unhappy with BOB running amuck after Mike turned good. (If BOB was Mike's familiar, he probably had him on something of a leash.) BOB wasn't paying his garmonbozia taxes, so the MFAP and "Mrs. Tremond" etc. were therefore helping the investigation of who killed Laura more than they might have otherwise.
Better on DVD: While it's fine on its own, most episodes seem to make up a single day of investigation. Some details from the first few days come in a little later, when you might have forgotten about it.
Big Lipped Alligator Moment: Season 2 episode 8 has a flashback of Ben and Jerry remembering a girl dancing around with a flashlight in their room as children. It's wordless, 4 frames per second, and goes on for over a minute. Hold on, Ben & Jerry?... Oh lord.
The singing scene with James, Donna and Maddy. Helped heaping them all onto the scrappy heap if they weren't there already.
As bizarre as the dream from "Zen, or the Skill to Catch a Killer" was, every element of it ends up returning and being important to the plot — with the exception of that shadow that passes behind the curtain.
Or is the shadow an exception at all? It looks an awful lot like the outline of a certain ring (viewed from above) that shows up in FWWM, which is heavily implied to be related to the Man From Another Place...
Canon Sue: No matter how you look at it, Cooper is a rather idealized character: intelligent, educated, physically fit, gregarious, charming, compassionate, well-liked by just about everyone he meets and praised by every police officer in the show as an excellent FBI agent. David Lynch also admitted that Cooper is at least partly inspired by Lynch himself, noting that "He says a lot of the things I say". So one could not unreasonably interpret Cooper as Lynch's idealized self-insert character. Unlike most examples of the trope, however, Cooper is not disliked by the fanbase because, being loosely based on David Lynch, he's also an eccentric Cloud Cuckoolander, which most viewers find endearing.
Creator's Pet: David Lynch liked Joan Chen's performance, which is why she gets a lot of focus despite not being very popular with fans.
Crowning Music of Awesome: The soundtrack, really. Good thing too, because most of it consists of a few tracks played over and over in each episode, and if it weren't so good it would drive people crazy. Now has it's own page.
Ensemble Dark Horse: Audrey is one of, if probably not THE most popular character aside from ol' Coop.
Gordon Cole, Albert Rosenfield, and Maddie Ferguson all have pretty big fanbases despite not appearing that much.
Fan-Preferred Couple: The Cooper and Audrey pairing was preferred not only by fans, but by Lynch himself; explicit references were written out of the script at Kyle MacLachlan's objection to their relationship. Both were later given other (and fan-reviled) love interests in the second season.
It's rumoured that the decision not to move forward with the Cooper and Audrey romance was down to Lara Flynn Boyle (who was involved with Kyle at the time). It was confirmed by the producer-writer Robert Engels.
It Was His Sled: Mostly averted, but those who have never seen the show should still be wary of spoilers. Many fans who saw it when it first aired believe the show is now too old for anything to be a spoiler, despite the fact that many new fans, too young to have seen it the first time, are trying to catch up in preparation for Season 3 (or because they became curious after playing Deadly Premonition).
Jerkass Woobie: Leo arguably becomes this over the course of his captivity in Windom Earle's cabin, during which he comes to understand firsthand the sort of horrifying abuse he inflicted upon Shelly. See Redemption Equals Death below.
Twin Peaks is currently a running joke on the TV Tropes Fora, where it is regularly mentioned among anime. (The reason for this is that someone once recommended this in an anime recommendations thread where the original poster didn't explicitly ask for anime.)
One-Scene Wonder: Loads of these in the movie. David Bowie shows up for all of a minute as Agent Jeffries (whose role in the shooting script was slightly larger), Harry Dean Stanton as a bizarre trailer park landlord, etc.
Jimmy Scott only shows up in the last episode — in one of the most haunting scenes in the series.
Replacement Scrappy: Annie Blackburn, who was wheeled in out of nowhere purely to supplant Audrey as Cooper's love interest. Her winning the Miss Twin Peaks pageant is likely to produce the same reaction from viewers that it did from Mayor Milford: "She's been living in this town about fifteen minutes!"
Rescued from the Scrappy Heap: Almost. After spending Season One as a weak-willed pawn being manipulated by Catherine and Ben Horne before running crying to Sheriff Truman, it is revealed that Josie has secretly been working with Ben to frame Catherine for the mill fire, and also had a hand in her husband's death, which gave her the mill in the first place. Then, in the following season, it is discovered that Josie did all this at the behest of another person, turning her back into the easily manipulated victim. One step forwards, two steps back.
Romantic Plot Tumor: Several. Primarily to blame for the general consensus that the second season would've been much better if it had been half as long.
The Scrappy: James Hurley (for being monumentally stupid, even by the standards of Twin Peaks teenagers) and Josie Packard (for being a hysterical victim and nothing else); take your pick. Or Nadine. Annie and John Justice Wheeler, especially if you're a Cooper/Audrey fan.
Lana Budding Milford also gets a lot of flack.
Arguably the series' biggest Scrappy is Evelyn Marsh, who served no purpose to the main storyline and was probably only added to write James off the show.
Seasonal Rot: It is generally agreed that the series loses focus after the main story arc is resolved in episode 8 of season 2. A new, related story arc emerges in the rest of the second season, but much of it suffers from having been neglected by Lynch and left to less competent writers and directors, causing a vast drop in quality and major inconsistencies in characterization. Kyle MacLachlan became impatient with Lynch's non-involvement and cast member Kimmy Robertson admits to having stopped watching due to Seasonal Rot.