The Animaniacs direct-to-video movie Wakko's Wish is an affectionate parody of animated musicals. note The funny part is that Steven Spielberg, who was the executive producer of Animaniacs (but not this movie), was also the producer of another animated musical.
Also they parodied Power Rangers with "Super Strong Warner Siblings", even getting the likeness of the command center down accurately.
Archer is an affectionate parody and deconstruction of James Bond and spy fiction in general.
Then there's "The Ember Island Players". How can you not love a show that parodies itself? The whole episode is the writers poking fun at the plotholes and contrivances from previous episodes.
Buzz Lightyear of Star Command, given that it is intended to be the in-universe cartoon the Buzz Lightyear toys are based on in the Toy Story movies, happens to be a warm love letter to pretty much every Merchandise-Driven action cartoon of the 1980s and 1990s.
The Critic (not Jay Sherman, but the Oscar-winning animated short starring Mel Brooks) is an affectionate parody of the works of Norman McLaren.
Danny Phantom is an affectionate parody of Silver Age comics, with a teensy bit of Golden Age and Bronze Age thrown in for good measure. For an animated media and not a printed media, the odd usage of 'POW!'s and 'WHAM!'s really accentuates this.
In general, the majority of the shorts on DC Nation were lighthearted and comedic depictions of numerous DC Comics characters, but one specific example was the New Teen Titans short "Kidz Korner 4 Kidz", which parodies educational shows for little kids like Sesame Street and Mister Rogers' Neighborhood.
Duck Dodgers featured an episode that not only parodied Samurai Jack—Dodgers dreaming he's Samurai Quack—but the dream sequence itself was directed by SJ creator Genndy Tartakovsky and featured Mako as the voice of Quack's adversary Achoo.
Another episode featured an incredibly close to its source parody of Green Lantern, complete with Kilowog, Ch'p, Ganthet, Sinestro, and more.
The show itself is an affectionate parody of sci-fi has a whole, and the protagonist's name is a parody of Buck Rogers.
DuckTales (1987) had Gizmoduck, an affectionate parody of RoboCop. He was even named Roboduck in foreign dubs. Later became more like Superman when he appeared on the sister show Darkwing Duck which itself was of course an affectionate parody of Batman.
Ever After High pokes fun at the awful parts of Fairy Tales while maintaining an upbeat and cheery attitude.
The Fairly OddParents!movie, Channel Chasers, is all about this as Timmy, Cosmo, Wanda and Vicky go through various parodies of popular shows. It was finally lampshaded in The Simpsons parody with Timmy writing on the blackboard "This is the sincerest form of flattery".
The show also has the recurring character of Cat-Man, voiced by Adam West; an affectionate parody of his earlier role as TV's Batman.
The jokes on Family Guy deviate from random ridicule to Affectionate Parody, and most of them are pretty good mixtures of both.
One of the most affectionate of them, however, would have to be "My Drunken Irish Dad" (as opposed to "The Freakin' FCC"), which is essentially a giant Take That! to, well, the Federal Communications Commission). Except that it turns out the FCC actually liked it.
The Freakazoid! segment "Toby Danger" parodied Jonny Quest TOS. They even went so far as to get Don Messick (Benton Quest) and Granville Van Dusen (Race Bannon) to do the voices of their parody characters.
Futurama is overall an affectionate parody of science fiction, and pop culture in general.
They assembled the entire (and then-living) cast of Star Trek: The Original Series for the episode "Where No Fan Has Gone Before", and spent 23 minutes lovingly mocking the show. Most of Futurama's writers are huge Star Trek fans, though series creator Matt Groening insists he's never seen an episode.
Except for James Doohan, who was replaced with Welshy. Briefly.
The character of Zapp Brannigan is an Affectionate Parody of Captain Kirk from Star Trek: The Original Series series. In a DVD commentary, producer David X. Cohen said his instructions to the writers when they sketched dialogue for Brannigan was, "Imagine if William Shatner actually captained the Starship Enterprise".
The Grim Adventures of Billy & Mandy is fond of this trope. They parody all the time and end up not making it look worse. A particularly affectionate one was "Hokey Monsters", a Pokémon parody, where they make it a card game and bring them to life. They pick at a few aspects of it but in the end it said Pokémon was still awesome. They've done many many others like Mary Poppins and Fantasia's "Night on Bald Mountain" segment.
Kim Possible seems to have been designed from the outset to ask the question "What if Buffy the Vampire Slayer was James Bond", leading to an "affectionate parody of spy movie conventions and superheroes" as part of its central concept.
Kim Possible did an affectionate parody of the 1960s Batman franchise with The Fearless Ferret, whose actor, Timothy North (voiced by Adam West), ended up being a space-case who thought the TV show was real. They also used the episode to poke fun at the upside-down kiss from Spider-Man 1.
The episode contained another level of affectionate parody, since it featured Ron as the young successor to a costumed legacy, with the original hero giving him constant advice and reprimands via radio. Ron's voice actor, Will Friedle, also voiced Terry McGinnis on Batman Beyond.
Nor was this Adam West's first go-round with such things, as on Batman: The Animated Series, he voiced the actor who played The Grey Ghost, a somewhat campy and clichéd costumed vigilante hero. Other appearances of the character implied that The Grey Ghost may have shared some of West's Large Ham tendencies.
Most of MAD is Affectionate Parody of nearly anything that's been popular in the past 10 years.
Metalocalypse, the parody of death metal whose soundtrack album made those in the same genre it parodies stop and take notes. It helps that the creator is a huge fan of the music, even including other parodies of the genre in his previous show, Home Movies.
The Powerpuff Girls (1998) episode "I See a Funny Cartoon in Your Future" spoofs Rocky and Bullwinkle and includes not only a caricature of Jay Ward at the end but has June Foray (Rocky, Natasha) as the voice of the ep's villain.
Also of note is their episode parodying The Beatles, which was full of jokes and references that made it clear that they were very familiar with the band.
ReBoot featured at least one affectionate parody in "virtually" every episode. One of the ways they can do this is the nature of the Games, where it transforms an area of Mainframe and comes with its own built-in story. But one interesting thing they did was that each parody flowed with the theme of the episode or was merely a fun backdrop to the main story. It is most notable in the third season, where every episode owes something to some franchise or genre. Just in the first half: Evil Dead, Looney Tunes, James Bond, Mortal Kombat, Braveheart/Xena: Warrior Princess/Dungeons & Dragons, Star Trek/Comic Books, The Prisoner, Spaghetti Westerns and Pirate/Great Escape.
Robot Chicken had parodied Star Wars and demonstrated more knowledge of and reverence for the originals than most, including character names and terms that aren't mentioned in the movies.
Saturday Morning All Star Hits! is presented as episodes of a Show Within a Show where segments of animation are interspersed with live-action segments of hosts introducing them. The shows are parodies of Saturday morning cartoons of the 80s and 90s, parodying the style and culture of the time.
"Homer's Barbershop Quartet" is an Affectionate Parody of the career of The Beatles in the form of Homer's 1980s barbershop quartet, the B'Sharps, that takes the world by storm in a similar fashion to the way the Beatles did. The career of the B'Sharps mirrors that of the Beatles in almost every way, including similar controversies, the complete hysteria surrounding them and band meltdowns. The producers even persuaded George Harrison to play along, giving him the perfect closing line; as he watches the B'Sharps imitate the famous last gig on the rooftop of Apple Corps that the Beatles played, he acerbically mutters, "It's Been Done", and drives off.
In "Angry Dad: The Movie", the titular short film is nominated for an award. One of the other contenders is a Claymation short called Willis and Crumble, a parody of Wallace & Gromit and in particular The Curse of the Were-Rabbit. Nick Park himself makes a Celebrity Cameo as the creator of the short and shakes hands with Lisa, who says it would be an honour to lose to him.
Even before that, in the show's 1st season, they also made an affectionated parody of Kaiju and Toku tropes with the episode "Mecha Streisand", showing their appreciation for Japanese pop culture.
South Park has also affectionately parodied The Simpsons in a memorable season 6 episode entitled "Simpsons Already Did It" that poked fun at how hard it was to come up with new plotlines when The Simpsons had already done so many.
In the "Coon and Friends" trilogy, this is done twice between Cartman and Cthulhu: one, a tribute to My Neighbor Totoro, and the other is a nod to the Chuck Jones cartoon "Feed the Kitty". The original "Coon" episode also parodies The Dark Knight in the beginning.
A meta-example: the 20+ minute animation "Trey Gets Stoned" is one of both the show itself (seriously, the animation is indistinguishable) and Trey Parker and Matt Stone. Not surprising, since it was made by several fans.
Star Trek: Lower Decks: This is a show that is best appreciated by Trekkies as the sheer number of references, mythology gags, and Easter Eggs can only be appreciated by a super fan of every series. However, it also lampshades how miserable and dangerous being a Red Shirt on a Starfleet vessel probably would be.
Star vs. the Forces of Evil is an affectionate parody of the Magical Girl genre. Star Butterfly is a princess from another dimension, and has a magical wand that looks like a mashup of several wands other magicalgirls use. However whenever she casts a spell it usually has disastrous results, but she also fights monsters with her bare fists.
The Teen Titans (2003) episode "For Real" includes shots of people commenting on the trials over the internet in what can only be an affectionate jab at series fans, and at shippers in particular.
is an affectionate parody of Kirk Douglas.