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.
Designated Hero: Excel does heroic things from time to time, but she is still working for an evil organization. Meanwhile, the City Defense Force (particularly Iwata) think they are working for the good of the city, but do as much harm as good.
It's more mixed up in the manga, where ACROSS doesn't really qualify as either good or evil organization (the world is definately just as corrupt as Il Palazzo declares, though he's hardly the best person to fix the matter), while the civil servants really have no illusion about Dr. Kabapu's morals (or lack thereof), either.
Author's Saving Throw: Revealing that Dr. Shioji only likes to watch little girls because it gives him some sort of peace, instead of being a full blown pedophile, just as he was becoming more important to the main plot, was so this. The expanded explanation is that his mother left him with a skewed view on adult women, but was inspired by the innocence of his young cousin, now that she is grown he is simply trying to find that inspiring innocence elsewhwere.
Near the climax of the Manga Shioji finds out that his "mother" was a third Ropponmatsu unit built by his Father, and at the very end it appears that he is coming to terms with his foibles - he acts far more mellow and appreciative of Umi.
Crack is Cheaper: With earlier volumes of the manga starting to go out of print, individual tankoban have been getting pretty pricey as of late.
Les Yay: Excel and Hyatt, obviously. Also, Elgala gets very touchy-feely with Excel when she's drunk, even though her "innermost thoughts" claims that she does not swing that way. Excel invariably retaliates with violence.
Anticlimax Boss: That Man took half the series to beat, while the other members of the ACROSS Six are quickly beaten in a quick gag in the final episode.
Better on DVD: Behind all the frenetic hyperactivity and deluge of jokes and refrences IS an actual ongoing story that develops from episode to episode with some surprisingly intricate detail, and its much easier to catch while viewing the episodes close together.
Crosses the Line Twice: Episode 26 (titled "Going Too Far" and intentionally desgined to make use of this trope), as well as anything involving Shiouji.
Fridge Horror: When Ropponmatsu II starts acting rather intrusive towards Excel, we see Hyatt watching the two before the Relax-o-Vision starts. After that, we return to the same shot, with Hyatt sitting in the exact same position, apparently having watched as Excel lost "... a bunch of things".
Genius Bonus: The references to obscure anime. Unless you're incredibly well-versed in anime from the '70s and '80s, chances are at least something will go over your head.
Les Yay: Besides one episode entirely dedicated to parodying the Yuri Genre, Excel and Hyatt are shown to share a bed, been through one rather extreme case of body-heat sharing, and when Lord Il Pallazo abandoned and nearly killed Excel for real, Hyatt cannot stop thinking about Excel even though she was ordered to forget about her.
Woolseyism: Quite a few examples in the English dub by ADV Films:
In "The Woman From Mars", Watanabe says, "Surely you can see that!" In the original Japanese, Iwata replies (paraphrased), "But my name's Iwata." In the dub, they used this opportunity to make an Airplane! reference: "Don't call me Shirley; my name's Iwata."
In "Big City Part II", there are two: Excel asks Nabeshin if her heart-rending emotion was okay; in the Japanese, Nabeshin enthusiastically replies, "It's good!" But in the English dub, Nabeshin replies in a disinterested tone, "Yeah, it's okay." Cue a disappointed Excel responding, "...Oh."
At the end of the episode, Kabapu asks the security team if they had fun on their field trip. The group replies, "It was the pits". In Japanese, Kabapu merely replies with a disappointed, "I see." In the dub, we get an MST reference, as Kabapu replies, "Oh, poopie."
In "Animation USA", Excel brings up Sailor Moon, and when the villain derides that show, Excel retorts that she was doing good until the show was cancelled a few years ago, a reference to the fact that Kotono Mitsuishi voiced both Excel and Sailor Moon. As this would make no sense in the dub, the line is changed to, "I wanted that job but it was dubbed in Canada!"