MAD's parody of The Morton Downey Jr. Show (Issue #286, April 1989), called "The Moron Downer Jr. Show" deserves a mention. In the end of the parody, the Pope himself visits the show to deliver a message. The comic ended with a full page splash of the Pope punching Morton in the teeth. Damn!
Issue #533, edited by "Weird Al" Yankovic, with several articles written by him. Two of the biggest names in satire, together at last.
On a meta level, issue #539 has something that many fans have been wanting for a long time: a front cover illustrated by Tom Richmond! (He got cover duties again for #548, and a third for #9 of the reboot [albeit In the Style of... Jack Davis].)
Also on a meta level... in March 2016, Al Jaffee was honored by Guinness Book of World Records for being the longest continuously working cartoonist, having not stopped since 1942!
Another meta-level awesome. Since they were classic Equal Opportunity Offenders, they incurred reams of lawsuits...and won most of them. The rulings in their favor could fill a small library when it comes to First Amendment protection of satire and parody.
Adding to the above; the whole magazine started out of anger at censorship. The anti-comics hysteria of the 1950's led to the Comics Code, which put most forms of comics out of business and forced the handful of survivors to severely Bowdlerize their content. One of the casualties was Gaines's Tales from the Crypt, deemed too dark and corrupting. Cue him taking that same Black Comedy, and applying it to a protected medium of satire and parody, which allowed for him to fire shots he couldn't even get away with when writing the Cryptkeeper.
During a company-wide vacation to the Dominican Republic, Bill Gaines discovered that there was only one subscriber in the entire country, and his subscription was going to expire that month. The entire Mad staff - artists, writers, editors, and Gaines himself piled into a bus and drove out to his house. Gaines knocked on the subscriber's door, and with the entire staff of the magazine looking on, presented him with a renewal notice.
On a meta-level, the Ghastlygun Tinies, a chilling and heart-wrenching parody of Edward Gorey's Gashlycrumb Tinies, is considered one of MAD's best articles in years. Not only is it a brutally effective bit of satire on school violence, but a lot of people, including The New York Times, took notice of how the article harkened back to MAD's heyday. Too bad MAD closed up shop a year later.
Bob the Builder OWNING Andrew W.K. in Destroy, Bob The Builder, Destroy is a good example.
"Once Upon A Toon", no question. How does MAD celebrate Cartoon Network's 20th birthday? With a character from pretty much every classic show uniting onceagain! Including Johnny Bravo, Dexter, Samurai Jack, Blossom, even Numbuh 1, and most of the time Cartoon Network just pretended KND didn't exist!
Even better, Dee Dee's Overly Long Gag about showing a "sample" of MADon a TV, in a recursive, matrioska-esque way further hammers down the point about how MAD's pop-cultural nature is the only way the characters could possibly have been acknowledged and gathered. As a Youtube commenter pointed out, this is 50% Biting-the-Hand Humor, and (much more subtly) 50% fan-trolling. And 100% awesome.
Rio-A: Blu gains Green Lantern powers, and gives rings to other flightless birds (Mordecai, Big Bird, etc.) to save Jewel. Awesome way to kick off Season 2.
Speaking of starting off season four with a boom (or should we say, a sonic rainboom?), MAD co-aired that sketch with "Rainbow Dashand Bernstein", a definite CMOA for the brony community. While the Fandom Nod in "My Little War Horse" was awesome and the other sketches never made fun of it, this sketch centered around MLP's male community in a positive light. But this line shows MAD has done their research:
Rainbow Dash: ...I can show you how to be 20% cooler by being a brony!
There's also the part where he was fighting dinosaurs.