You mentioned some truly great feats of animation, including and especially Gargoyles and Samurai Jack, which often don;t get the credit they deserve outside of fan-sites and critical journals. But understandably, there are a few that you missed, but I, being one of the Trio of Too-Much-Television, will rectify this problem.
AEON FLUX
MTV ventured into animation in 1991 with an anthology series called Liquid Television and hired a frustrated Rugrats animator Peter Chung to create a spy vs. spy-like short for the series. Chung created the impossibly svelte superspy Aeon Flux: a lanky, unbelievably flexible, dominatrix-clad anarchist fighting unclear missions in a futuristic world with incredibly dense detail. Throwing convention to the wind, Chung eschwed all familiar traits, including dialogue, explanation, believable architecture and clothing, heroic behavior, and most famously of all, ended all but 2 of his 6 shorts with Aeon's death (in the other 2 the story went on without her). The series was so popular, it was picked up for 10 half-hour episodes that gave cahracters names, voices, and storylines, but this didn't prevent the surrealist and multi-intepretive meanings and stories--as well as Aeon's death--from carrying over. Aeon Flux is probably the greatest underappreciated fetish icon since Julie Strain, her ability to inspire prepubescent perverts to masturbation rivals even that of Bettie Page.
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AQUA TEEN HUNGER FORCE
The powerhouse flagship of Cartoon Network, this nonsensical show is about a trio of superhero foodstuffs (A talking milkshake, a floating set of fries, and a rolling ball of meat) who sit in their run-down New Jersey house and bitch at each other while bizarre happenings go on around them. The true brilliance of this show is that it manages to be funny without letting the audience on to the most obviously subversive agenda of experimenting with post-narrative fiction. The show has become more and more absurd and indecipherable in the later years than its more accessible first season, and the movie version that exists is almost impossible to understand even for fans, but I think it's rare to find yourself laughing so hard at something that essentially doesn't make any sense.
BEAVIS & BUTT-HEAD
Yes, that's right, I said it, B&B is a great fucking cartoon, although it's almost impossible to see that now given the state of things. A show you either loved because you got it, or hated it because you couldn't see past the content, MTV's legendary show about two inhumanly moronic teenage metal heads getting into painfully dangerous self-destructive shenanigans is brilliant BECAUSE of it's emphasis on stupidity. A minimalist masterpiece of satire, B&B was all about the dual experience of visceral delight at sophomoric humor combined with the more profound pleasure at realizing how frighteningly familiar such commonplace idiocy really is. Unfortunately, pyromaniacal references and the unabashed displays of homemade drug abuse caused so much controversy that many episodes have been so severely truncated that even it's creator Mike Judge feels they no longer exist in their original uncensored form. Added to which, legal issues prevent the original music videos from being included in collections, which means no one outside of the original 1993-1997 run will ever be able to witness the full genius of such a stupid cartoon.
DARIA
Originally a marginal character on Beavis & Butt-Head, Daria Morgendorfer, a cynical, bespectacled teenage intelligentsia moved into a new town and her own series that seriously lambasted conformist ideology and role models through a combination of acerbic wit and mockery. The only truly sane member of her family, she befriends local outsider artist Jane Lane and together the two streamlined one of the most intelligent and captivating female-centered relationships since My So-Called Life (but with far less whining). Towards the final 2 seasons, the episodic adventures gave way to story arcs involving the complications of a boyfriend and his effect on their dynamic, and ended on a high note with 2 feature-length TV movies that sent the characters off into their uncertain futures, without inviting us to tag along. If only MTV could recapture the power that was once their animation department.
EXCEL SAGA
This hilarious product of a creative team of animators fueled by the contents of the local tap water, Excel Saga tells about an beautiful, idiotic but zealously optimistic college graduate named Excel who intentionally goes to work for a laconic evil genius bent on eventually conquering the world. She nevertheless fails often, but not before getting herself killed a few times and being revived by the universe, who abducts a Mexican construction worker living in Japan from his "Sexy wife" into herself as a boy toy. Fast, loud, out-of-control and not exatly being driven by a point, other than tormenting a poor dog who is their "emergency meal" in the case of being marooned, the high point for me was when Excel's first mission involved tracking down and killing the creator of her own series. Genius. Pure, warped, psychotic genius.
FLCL
A combination of mechanime and The Naked Gun, there has probably never been a weirder, more senseless cartoon than Fooley Cooley (not even Super Milk Chan). A beautiful but totally insane Looney Tunes acid-trip of woman named Haruko Haruna arrives on a futuristic Earth on a sentient Vespa motorcyle and sexually accosts (but not molests) a timid teenage boy in the middle of his vaporous relationship with a would-be girlfriend. Once strange, massive robots start emerging from his skull, things get weird as Haruna takes to bashing them with her buzzsaw Fender Stratocaster as the world becomes more and more threatened by the impending arrival of an unseen and unexplained space pirate named Medico Mechanica. Nothing makes sense, the story has no real resolution, and the animation is constantly interrupted by violent gunfights, car crashes, and competing styles interrupting the frame, it's still addicting to watch, and offers the most kick-ass J-Pop soundtrack of all time by a stellar band The Pillows. The soundtracks are worth buying independently of viewership.
FREAKAZOID
The team at WB animation decided that Animaniacs wasn't self-referential enough, so they created a show that existed solely for self-parody and postmodern humor. A computer geek named Dexter gets zapped by a government program and gets tranformed into Freakazoid, a blue-skinned, bride-of-Frankenstein-haired superhero whose undetermined powers factor marginally in his heroic exploits against some brilliantly designed but ridiculously inept villains. Freakazoid was accompanied by a variety of smaller sketches that sometimes bled into each other and crammed as much absurd and bizarre humor as they could into every minute. Cancelled after 2 seasons thanks to poor time slotting, it occasionally shows on Cartoon Network. In an inspired bit of brilliance, the late great Jonathan Harris (Dr. Smith of Lost in Space fame for those of us born before 1985) was cast as Freakazoid's manservant, and never did any character ever miss the chance to ask him "Werent you in that show with that robot?" Here's 2 samples of Freakazoid genius.
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INHUMANOIDS
A rarely-remembered entry in the heroic cartoons of the 1980s, Inhumanoids is not great for so much as the others here, but for its truly dusturbing content uncharacteristic for a decade devoid of animation chutzpah. An evil corporation digging far into the Earth unleashes a trio of gigantic malevolent indestructable monsters intent on conquest of the Earth: the molten Metlar, the tempermental plant creature Tendril and the mutant D'Compose. Only a team of dashing eco-scientists with the aid of Earth-friendly rock creatures can stop them. Unlike the shows of the day, the heroes barely managed any victories against their vicious and overwhelmingly powerful foes, and the depiction of evil corporate America is a retrospectively subversive addition to the Ayn Rand-worshipping decade of capitalist decadence. But the top honors go to D'Compose, the most gruesome cartoon charcter of all time: essentially a giant, mutated, sunlight-aversive Dinosaur skeleton who had the ability to hold captives in his exposed ribcage and turn them into zombies by prodding their faces with his thumbnail. The last 5 episodes have rarely been seen outside of their original broadcast and are absent from the DVD collection, although rumor has it Region 2 DVDs has them all.
THE PIRATES OF DARK WATER
Talk about a show that never got it's due, this was one of the most promising Saturday morning vehicles of the early 90s. On an Earthsea-like planet of Mer, a sentient, evil tar-like substance called Dark Water is eating the planet piece by piece, and a young overzealous adventurer named Ren has to team up with a gang of ragtag misfits and theives to hunt for the scattered mystical treasures that can stop it; of course, he's pursued by a grotesque villain named Bloth in a gargantuan ship Leviathan who wants the treasures for his own wealth. The show simply never got picked up after the first seasn leaving many of us to wonder "Hey, when's it coming back on?" Truly an underappreciated lost treasure.
THE VENTURE BROS.
I would explain this show, but then I'd have to spend five days talking about why the Johnny Quest-style adventure shows of the 1960s is important first. If you aren't familiar with Hanna-Barbera's old action cartoons, then you will never be able to appreciate the genius that is Venture Brothers.
By the by, Ren & Stimpy have already been mentioned.