No Need For Bushido, while technically set in imperial Japan, cheerfully features a hodgepodge of ninjas, Taoist monks, an order of scantily clad female assassins, giant anime-style swords (well, ok, one giant sword), Hong Kong kung-fu action movie fighting styles, and modern-day references. And TWO blind kick-ass fighters. Also, birdfish. (The NNFB fanmixes take this anachronism with modern day references even further, to absurd but often hilarious extremes)
Arthur, King of Time and Space gleefully throws the anachronisms into the "fairy tale" arc (the standard Arthurian romance with the standard medieval trappings) with two justifications: the author (and to a lesser extent, the characters) knows the sources are flawed and anachronistic in and of themselves, and half the anachronisms are Merlin's fault, since he has the gift of foresight (at one point, for example, using a fly swatter to kill a fairy spy).
Dinosaur Comics. While inherently unrealistic (talking dinosaurs), they oftentimes reference human events, which obviously would take place many millions of years in the future. This is often lampshaded.
There's anachronisms in every strip: The third panel has T-Rex about to step on a house that's next to a car, and the fourth panel has T-Rex about to step on a person.
In The Order of the Stick's Azure City, not only are there sewers, but there are three tunnels, clearly labeled "Ocean," "Anachronistic Sewage Plant," and "Obligatory Sewer-Themed Labyrinth." Such things have been lampshaded.
And in Cliffport, there's a municipal park. Amid high-rise buildings.
Redcloak: (...) but I'm the one who has to make the magical lightning-powered trains run on time.
The C.C.P.D., complete with sirens (on the horses), sketch artist and mayor yelling at Da Chief for failing to catch the murderer when elections are coming up, and underlings being yelled at by said cigar-smoking, coffee downing chief. One double serving of Anachronism Stew, coming right up.
It's subtle, but look at this comic. Where did Hayley get a metal detector? And more importantly, where was she keeping it? (Same questions apply to Roy and his sextant...)
Being set in the world of D&D v3.5, I'd imagine they kept them in their always-present-but-never-seen backpacks, capable of holding as many items of any dimensions as there are spaces on their character sheets and with the ability to protect their contents from damage of any kind, be it fire, water, acid, sudden force, etc. Would that all backpacks were D&D backpacks.
In Gunnerkrigg Court, Ms. Jones' students watch a documentary hologram about the founding of the Court. The characters in the hologram include a guy who looks like he stepped out of The Cavalier Years or The American Revolution, and another fellow wearing a modern trench coat, an article of clothing which wasn't introduced until World War I. Shortly afterwards, Jones points out that "this simulation is an artistic representation". Although she said that in regards to an indistinct glow, represented as such because they didn't know what it was. And present was also the man who designed robots. Maybe the others just liked to dress that way.
Hellbastard Comics starts with an alien war that interrupts Satan's viewing of Bridezillas in what is later revealed to be the pre-Napoleonic era and just gets better from there.
Blade Bunny takes place in a historical mashup of feudal Japan and ancient China, with robots one of which has futuristic guns and a BunnyGirl in a microskirt. Justified in that it's revealed that the robots and the BunnyGirl come from different dimensions.
ThisPenny Arcade comic has a flashback to 1988 showing characters using a Powerglove (introduced in 1989 and quickly flopped), reading Nintendo Power #31 (December, 1991), talking about Thunder Cats (ran from 1985-89), and drinking a New Coke (introduced in 1985 and quickly flopped). To be fair, the date is only implied, and everybody didn't immediately quit drinking New Coke, playing with Powergloves, or referencing cancelled cartoons. But the overall impression is a mishmash of things associated with the '80s, regardless of which part of the '80s (or early '90s) they actually came from.
Problem Sleuth: it's theoretically Prohibition-era, but the main characters play games from the Fifties, have 90s murals to ethnic diversity on their walls, and check Gamefaqs to solve the hardest puzzles.
Nimona often sees combinations of fantasy-medieval and sci-fi themes. The secondary main character, Ballister Blackheart, is a Black Knight with a robotic arm.
GastroPhobia is set in Ancient Greece and has things like banks, dining-and-dashing, XP points, and quotes of Friedrich Nietzsche. This is lampshaded in a gag strip when Philia calls Klepto's drink, a Beijing Peach, anachronistic. The comic also parodies this trope by having the map of Greece◊ be a recolored map of Texas. Some parts are justified due to the machinations of the cast's Time Travel-capable characters ( Lord Nightsorrow explicitly claims to have brought back Halloween with him).