Kevin is something of a sociopath that doesn't miss his home and zaps things to get attention (S2Ep9). Let's not get started on Kevin and Mike from the first season.
Angst? What Angst?: Kevin is in a world full of people he doesn't know, his sole companion from his old world is his dog, he's cut off from all that is familiar, and he's being forced into war. Possibly falls under Rule of Funny, as the only time he had the opportunity to go back he stayed because his mom told him to do his homework and take out the trash.
Ensemble Darkhorse: Fans looking back on the show seem to take a liking to Simon Belmont. Reasons for this include: being just more interesting than Kevin, he was flawed and thus seemed more like a real person. Showing character development as the show went on, such as: gradually warming up to Kevin season by season. (That is, if you do get past on how totally different he was than in the original source, incredibly ironic when you notice that Simon usually gets touted as the biggest case of You Don't Look Like You by the original game fans)
Gameboy for having his moments of snark.
Also Mike, who got only one episode but was a major part of a very emotionally-driven episode.
Mother Brain seems to have developed a following in her own right.
Ham and Cheese: Levi Stubbs as Mother Brain. The show is worth watching just for his performance. This is probably the reason why she qualifies as an Ensemble Darkhorse.
Reinhardt Schneider, one of the protagonists in Castlevania 64 and Castlevania: Legacy of Darkness, bears some resemblance to the Captain N version of Simon Belmont. Both have blond hair and wear blue coats with fuzzy collars.
Lana isn't based on any particular game character, but she still manages to bear a resemblence to one — Alis Landale from Phantasy Star I, a Sega game, who can even become queen at game's end.
And more recently, there's a new playable heroine in Hyrule Warriors named Lana!
Simon's voice actor would later go on to play a prominent vampire character in the Underworld film series.
Donkey Kong is played by Gary Chalk. It wouldn't be the lasttime he'd play a famous gorilla.
Kevin and Mike have shades. For the whole show it seems like King Hippo and Eggplant Wizard are an old bickering couple with some slight abuse issues. This is kind of helped by the fact when they go undercover one is dressed as a woman.
Kevin and Link, in the Zelda crossover episodes.
I Am Not Shazam: Kid Icarus/Pit. One of the stronger indicators that the people working on the show had never played any of the games.
Narm Charm: This trope and the very premise of the show (kid gets warped into the world of video games and meets many NES characters) are arguably the only reason this show has the admittedly small following it does.
The Scrappy: Difficult to say, given the multiple bastardizations amongst the supporting cast. But even fans of the show generally hate Gameboy and Kid Icarus.
Seasonal Rot: Among fans, the third and final season is the least regarded. Animation took a major step down and the running time was cut to eleven minutes so that it could be paired with Super Mario World. Additionally, Simon and Mega Man were used less often (a result of Konami and Capcom, respectively, owning those characters and being entitled to royalties).
Special Effect Failure: The episode "How's Bayou?" wasn't quite finished when it first aired, and as a result, several shots were missing their backgrounds. Reruns of the episode had the backgrounds intact, but for some reason, the DVD set uses the original, unfinished version, as does the version on Jaroo (the "Hulu for kids' shows" site).
The badly-drawn electrical current in the intro, which is followed by an Art Shift to ugly, monochrome CGI. Both of these were fixed in the Season 2 intro.
Squick: The episode "Mr. and Mrs. Mother Brain". Simon ends up under the influence of a love arrow and falls for Mother Brain. Alright, that's bad enough, but later on, Mother Brain ends up falling in love with him. Okay, really gross, but then they become engaged and almost married, and somewhere in between those two events Simon imagines them having children! Granted, this is all fixed by the end of the episode, but still! Gah!
It's only for about a few seconds, but in "A Nightmare on Mother Brain Street", Princess Lana was shown having Mother Brain's face! Doubles as Nightmare Fuel, even in-universe.
Kongoland and Donkey Kong are pushed in the opening credits of the first season as heavily as Kid Icarus, Castlevania, Mega Man and Metroid. All the other worlds listed produce major recurring characters, but Donkey Kong? Of course not. He shows up five times in the whole series and that's it.
With Punch-Out's King Hippo as one of the main villains you'd expect a Punch-Out episode or at least other characters from the game to appear. Nope! All you get is a one minute scene in one episode of King Hippo's world, featuring no other game characters and that's it!
More importantly, why couldn't Link join the N-Team in season 2 instead of Gameboy?
Ugly Cute: For all its horror value, "Mr. and Mrs. Mother Brain" does give us the strangely adorable baby brains.
What an Idiot: Wishful Thinking has the N-Team coming across a magic lamp with a Genie that can grant any wish. And while Lana briefly considers it, no one uses any wishes to defeat Mother Brain or wish for King Charles to return.
The N-Team are gone for 3 weeks during their quest to find the Warp of Life in Happy Birthday Mega Man. Despite that absence, Mother Brain and her henchmen don't even attempt to conquer Videoland, nor does the N-Team acknowledge the possibility or even mentioning the villains at all.
Kevin completely forgetting about the pepper in Burger Time.