In The Adventures of Dr. McNinja, Gordito quotes part of The Gunslinger's Creed, which convinces Dan to allow him to keep his revolvers. Dark Smoke Puncher points this out, which Gordito responds by noting that he knows an awful lot about The Dark Towers.
Ctrl+Alt+Del featured a character strikingly similar in appearance to Tyler Durden from the movie Fight Club speaking for the character Ethan with the line "he fell down some stairs" to explain to a doctor the reasoning behind some suspicious facial trauma.
Similarly, there's a strip where Ethan imagines himself in a "happy place"—a frozen cave with Ted's hated pet penguin, and a giant mallet. The penguin's even panicking and thinking, "...slide?"
The characters play Candy-Land Adventures in #1453 and #1460. Candy Land is a simple children's game. Candy-Land Adventures transforms this game into an RPG like Dungeons & Dragons, complete with rolling dice, fighting monsters, and arguing about the rules. Roles include Peppermint Paladin and Rogue of Red Hots.
In a recent arc, a character Richek reveals that he's seen the grim reaper numerous times and considers him somewhat of a friend, but no one else has ever seen him, and he doesn't know his name. What does he call his tall, rabbitty pal? "Harvey!"
This installment of. The same arc shouts out to Redwall again with the fact that Sue is in "Saint Ninian's Hospital.
Lightbringer does it a lot. Main character quotes Watchmen, his friend once dressed-up as a spoiler, and when he asked another character about how can he be sure he don't kill anybody, the answer he get was Cassandra Cain
Ménage ŕ 3 features a fair number of shout-outs, mostly to pop culture; see the comic's own page. Just for one, Gary often wears shirts with various symbols from retro TV shows, like ReBoot, as well as newer but still rather obscure shows, like Code Lyoko.
In Mob Ties, you can play a fun game called the Mob TiesShout-Out drinking game. Take a shot every time you spot a Shout-Out on a strip. Just be sure to play it someplace where you can get emergency medical attention very quickly, or you may be dead before you get halfway through the archives.
Narbonic has so many shout outs and obscure references that one has to read the Director's Cut version to find all of them. Shaenon Garrity lists everything from other webcomics to manga to Shakespeare.
Early in the "A World Without Piffany" arc in Nodwick, the hapless henchman plummets between realities... passing, as he does, a police box with a scarf stuck in the door. The author, Aaron Williams, seems to like Who shoutouts, since he has also had an elven healer mistakenly refer to Piffany as "Romana", and then offer her a jelly baby. (The latter in a parody of the Dungeons & Dragons movie, where the equivalent character was in fact played by Tom Baker.) A further Doctor Who parody comes with the wizards whose psyches reside within the Orb of Omnescience; their appearances and personalities come from the Third, Fourth and Fifth Doctors, plus Romana.
Pv P is rather fond of pop culture and video game references. In addition, this strip was an obvious shout out to the Holiday Wars arc of Sluggy Freelance.
Questionable Content is also fond of Shout Outs at times. Most prominent victim is probably Dune (The booze is life!) though also animes are referenced at times, such as a crazy chick on vespa hitting men at random.
There's also this shout-out to Evangelion over here
Spinnerette has things like a security guard who pulls off a Crowning Moment Of Awesome showing up with "CMOA" on his jacket in his next appearance, and a Canadian superhero known as The Werewolf of London, Ontario. Also, a villainess learns magic from a Dungeons & Dragons rulebook, and you would not believe how often Marvel and DC are mentioned (especially Marvel, because it's...kind of obvious the writer is a fan of Spider-Man).
Super Stupor is pretty blatant when they do a shout out to the TV Tropes Wiki itself, in this strip.
There are plenty to found in Toki No Tanaka, largely to Nintendo games and exclusively to Japanese media (funnily enough).
Too Much Information has plenty of sci-fi refs, but the serious Shout-Out is given by Gina Gibs, the mother of main character Ace (who actually is The Ace). Years ago we learned she spoke lots of dialects of four Oriental languages, and has served in the Air Force in Korea as a translator when Ace was little. Then we learned she picked up some other languages 'when she was bored', like Arabic. Then she re-enlisted in the Air Force at the height of the Iraq War. What does she really do for the Air Force? Something else entirely.
Also, there's the "Hitmontop" worker. In addition to spinning around on his head, he attempts to use triple-kick on Slick. Later, Slick is told to "mash the B button" to stop one of the goo creatures from evolving.
When Red Mage tells Fighter to "Make your swords as things unto chainsaws", the card he uses to do it is an Exalted charm-tree card; the name and effect refer to a (now fixed) exploit with Exalted's Glorious Solar Saber charm where you could theoretically conjure a sword capable of making infinite attacks in a single second, which fans affectionately called the Glorious Chainsaw Method.
21st Century Fox is full of various references and shout outs, to the point we'd need an entire page just to list them. The most common ones include classic songs ("White Cliffs of Dover"), various Sci-Fi movies and the works of Gilbert and Sullivan.