Fridge Logic: One early story arc in the comic had Howard running for president, but since he comes from another dimension, he's not a United States citizen, and is therefore not allowed to run for president in the first place.
Marvel's editors made Howard start wearing pants to prevent Disney from suing on the grounds of him looking too similar to Donald Duck. Now that Disney owns Marvel, that's probably not an issue.
There's actually a character named Scrounge McDrake, a parody of Disney character, Scrooge McDuck, long before Disney bought Marvel.
Also, Ludwig von Cluck is a parody of Ludwig von Drake, another Disney character.
Jerkass Woobie: As Howard himself is quick to point out, he was plucked from his home and thrown into a world where he does not belong, doesn't understand, and more often than not, isn't wanted. Anyone would be cranky in that situation.
Tear Jerker: Issue #26 of the original run, which ends with Paul Same getting hit by a stray bullet after a convoluted sequence of events put him in the wrong place at the wrong time. At the same time, Winda Wester is badly beaten by a violent drunk, and both are hospitalized with Howard sitting in the waiting room, not knowing when (or if) they'll get better.
The Woobie: All Howard has ever wanted was to go home only to be constantly denied. In his later series he starts to realize that even if he were to get home at this point, it wouldn't be home anymore.
Adaptation Displacement: Would Howard the Duck be as famous if it wasn't for this bomb of a movie? It's quite possible that the comics made after the movie wouldn't still be around if people didn't read them to...see them mock the movie regularly!
Awesome Music: Though the film is unpopular, the Thomas Dolby-produced soundtrack is well-regarded by his fans, especially the song "Don't Turn Away." Also John Barry's score and Sylvester Levay's music for the scene with Howard's flying the Utralight. Intrada issued a 3-CD set in 2019 (with Barry's complete score, Levay's additional music, Thomas Dolby's songs and MCA soundtrack album in its CD debut). A Cult Soundtrack if ever there was one.
Fridge Horror: Howard willingly decided to leave DuckWorld behind. What will happen to his family and friends, those who don't know what happened?
Ham and Cheese: Once Dr. Jenning has his body taken over by the Dark Overlord, Jeffrey Jones starts playing the villain way over the top. Amusingly enough, Howard and Beverly don't take him seriously, even having a Face Palm at some point. On the other hand, they are trying their hardest not to be scared and try to lighten the situation, especially with a murdering sociopathic alien for company.
Special Effect Failure: This trope was a particular factor in the film's poor critical reception, as critics couldn't believe the then-huge $37 million production budget and Lucasfilm backing couldn't buy topflight effects work. It didn't help that some of the rival films at the August 1986 box office served up stunning effects on substantially lower budgets — the combined production budgets of Aliens and The Fly (1986) tallied up to less than this film's.
Howard is a duck? No way, he is a small person in a suit! Ironically, in the movie (and a few times in the comics), he is actually mistaken several times for a small person in a suit! It was one of the first animatronics to be remotely controlled, which was a new innovation at that time. Universal's marketing department was apparently aware of how bad Howard looked in practice — the suit suffered a lot of issues during both pre-production and while filming (including several incidents where the suits exploded or lost their feathers), because the trailers, posters, etc. made a concerted effort not to show much of Howard beyond his hands and feet.
Mostly averted with the Dark Overlord, who is considered to be the best effect in the film by a few critics who bashed the film — but there are a couple of shots where the stop-motion puppet is poorly composited into the live-action footage, particularly when Howard zaps it with the laser.
Spiritual Licensee: Some would say the 2012 movie Ted showed how to do the basic urban fantasy concept of the property right on film.
The near-sex scene between Howard and Beverly. Thankfully, it's interrupted. Lea Thompson, who is the one person who didn't disown the movie, admitted her daughters never finished the movie because "After the love scene with the duck, they turned it off. They will not turn it back on."
Also, the infamous "DuckTits" at the beginning of the film.
Took the Bad Film Seriously: As mentioned elsewhere, Lea Thompson owned her role and makes no apologies for it. During the finale, she very effectively transitions from grief at Howard's apparent death, to fear when it seems that he's survived but become the new host of the Dark Overlord, to relief and happiness when that's clearly not the case.
Uncanny Valley: Howard, thanks to his glassy-eyed, inexpressive animatronics, and the number of times that he's shown staring directly into the camera.
Uncertain Audience: Despite being rated "PG", and having lots of childish humor, the movie also contains lots of sexual humor and innuendo, including references to zoophilia.
What Do You Mean, It's for Kids?: The concept certainly sounds family-friendly enough, but the film itself, with its scenes of implicit violence, dark shots, explicit sexual sequences and horror movie twists and turns in the final act, clearly isn't. The Nostalgia Critic called out the MPAA for this, starting with the "duck tits", baffled by how the MPAA allowed "Daisy's knockers" into the film but barred human breasts. (It's a good thing Beverly's profession was changed from the comic book — where she's a nude model).