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.
Awesome Music: Besides the show's theme music, there's Dave Grusin's score for "The Night of the Puppeteer" (in particular Vivid's dance music - which, tellingly, was never tracked into any other episodes) and Richard Shores's cue for the fight between Jim and Titan in "The Night of the Eccentrics" (used in assorted season two episodes and a trailer for the series itself). Shores also composed a propulsive score for "The Night of the Firebrand" (with a variation of Artie's theme music so beloved by the music editors that it was tracked into "The Night of the Bubbling Death," which actually aired before the episode it was written for).
Narm: "The Night of the Dancing Death". Especially for anyone who knows anything about the real Camorra. The way Jim's amnesia is cured in "The Night of the Amnesiac" also falls into this category for some fans.
"The Night of the Wolf" has several shots of a more-than-obviously-stuffed canine.
The tank in "The Night of the Juggernaut" was called out by some press sources at the time of the episode's original airing for being rather poorly done; the tank is indeed embarrassing, both in its design (late 1960s racing stripes?) and in it being so slow Ironside could have outrun it. Without his wheelchair. (The tank in "The Night of the Freebooters," on the other hand, is far more convincing. And that was in season one, while the Juggernaut was for season four.)
In the robbery scene of "The Night of the Burning Diamond," some of the people "frozen" in time are more frozen than others, to put it politely.
The freeze-frames for "The Night of the Flaming Ghost" are uncharacteristically sloppy - the one for Act II (where an enemy knocks Jim out and sends him falling off a ledge) has a lag of a couple of seconds rather than have the section being filled in appearing immediately upon freezing, and the final pullback to show the complete collage is repeated (for the only time in the series) behind the end credits.
Tear Jerker: Artie's anguished reaction to apparently killing Jim in "The Night of the Death Masks."
They Changed It, Now It Sucks: Some fans think the shift to color was detrimental. Also, there are some who consider the nine Martin-less episodes in season four to be hardly worth watching. The decision to have the end credits for the final season's shows run over a standard collage rather than an episode-specific one (see the illustrations on the recap pages) also doesn't appeal to some viewers.
More than once a villainess is given much a lighter punishment than her male counterparts such as Morn in "The Night of the Flying Pie Plate," who gets a lighter sentence than her other conspirators - including her two sisters, who significantly didn't have Girl of the Week status, or even allowed to walk away scot-free, apparently simply because she is a beautiful woman. This is compounded at the end of "The Night of the Red-Eyed Madmen," when the villainess gives a rather insightful, moving speech about how she'd only wanted to be seen as more than "just a woman." This small step forward is promptly ignored in favor of having her and another woman fawn over a new dress and begin discussing how to look their best when the train pulls into Carson City.
The entire last scene of "The Night of the Firebrand" just drips with misogyny, as West and Gordon decide that Vixen O'Shaughnessy's punishment (for helping mastermind an attempted massacre at a military fort and a coup against Canada) is to be "forced to return to the feminine fold" so that she will "leave the fighting to us," by which they mean they're just going to make her return to the ladies' finishing school she escaped from. When she objects and goes into a Character Filibuster about all the wrongs that still need fighting against in the world, West basically gives her a Vulcan nerve pinch (a Running Gag in this episode) and reflects that he'd better tell the school's headmistress how to do it.
"The Night of the Tycoons" romps home with the gold in Misogynistic Episode Writing; other episodes have female villains, but there's an unpleasant tone throughout the episode suggesting women have no business being in charge of huge corporations, capped off by its tag scene with Lionel's fiancee Kyra booted off to the kitchen and Jim telling him he's got to keep these women in their place.
All that said, there are exceptions: Lady Beatrice in "The Night of the Two-Legged Buffalo," Posey in "The Night of the Poisonous Posey" (although captured offscreen), Laurette in "The Night of the Winged Terror, Part 2" and most notably Astarte in "The Night of the Druid's Blood" - Jim makes it very clear to Astarte that she'll hang for her crimes [including helping to murder a beloved professor of his] and he won't mourn her.