Ear Worm: The theme song. Partially due to the presence of certain siblings of certain controversial Disney personalities. But even if you hate the song, it's undeniably catchy... which makes it much more of an Ear Worm if you do hate it.
Ensemble Darkhorse: Fujimoto. Despite (or even because of) the fact that he's a henpecked, crotchety, and overprotective father, two-thirds of the small but growing fanwork base involves him.
You could also say that it's because he's an adorable Cloudcuckoolander and overprotective but loving father.
Or because he has a mostly untouched backstory as a former human who became an undying sorcerer of the sea.
Or because he's funny as hell.
Or just that he can be creepy and adorkable at the same time (at least in the English dub, since some of it has to do with his voice). For instance: "Respect your father!" (said menacingly, the creeper part) -> essentially a pratfall (dorky) -> "Girls, I'm trying to save your sister!" (said pleadingly/worriedly, kinda cute as a protective dad thing).
Harsher in Hindsight: The March 2011 8.9 earthquake in Tohoku had the ocean sweeping over elevated roads in the same fashion as the film. Nobody dying, and everyone shrugging it off as a 2.0 earthquake? ....yeeeeeeeeeaah.... not really. Makes it a "Funny Aneurysm" Moment in the film, too.
Matt Damon and Tina Fey's characters are a married couple, although are in separate distance from each other. In the new season of 30 Rock, Tina Fey and Matt Damon play characters who are dating each other.
Liam Neeson playing a loving, extremely protective father in this movie...then playing an extremely violent version of the same archetype in Taken.
Adventure Time fans might notice one of Sosuke's peers holding a green plush elephant that resembles Tree Trunks with tusks, although Adventure Time had yet to become an actual show when Ponyo premiered.
The "Ponyo loves" fancomic, which has been cloned into many other fandoms as a Counterpart Comparison of sorts. In it a character talks about the people and things they love in an animated fashion, only to get a serious face when introduced to an antagonistic/oppressive character and express their love of revolution.
Leaving five-year-old children alone and unsupervised (in the middle of a typhoon, no less!) could be considered criminal neglect in some jurisdictions. Still, it can be considered as Lisa choosing the lesser of two evils — either bring them with her where they'd all easily be swept away by a particularly bad wave, or let them stay on high ground in the comparatively safe house.
Why isn't staying at home an option? Did the old people at the retirement home at least give her a light lecture? They've lived a full life, but if anything happens to Lisa, or her husband at sea during the typhoon, the two kids wouldn't last long.
The reason why she left them to go to the retirement home may have been the movie's way of reflecting the Japanese value that the young should take care of the elderly, no matter the circumstances. A strong case of Values Dissonance, especially since in Western culture it's viewed as the other way around.