Word of God is that different fonts represent different accents.
In The Order of the Stick a mysterious voice is found out to be evil because it speaks in red-and-black speech balloons.
Pretty much any kind of unusual or otherworldly speech pattern is conveyed by coloured text balloons. The lich Xykon's speech balloon is black with white font to get that "undead evil power reverb" feeling. Fiends and outsiders in general usually have coloured speech balloons that correspond to their primary colours. After a character makes a Deal with the Devil and gains evil power, their speech balloon turns black, with the secondary colour being the same as the colour of their magic.
A panel that emphasizes Roy's superfluousness to the Order's current dilemma has a speech bubble cover his body.
Dominic Deegan: Oracle for Hire has used sequences that break the comic strip, once to symbolize a breakdown of reality, other times of the mind. (The mouth-things and mosaics in the former are completely normal — the place depicted is weird.) More recently, as of this writing Dominic pulled a spell he'd been fighting with in his mind outside of his body, and for the next few days, has been fighting with it outside the boundaries of the panels.
In Achewood, Chucklebot (a robot, duh) speaks in a digital font. Blister, a ghost squirrel, speaks in unpunctuated block capitals. The most notable example, though, is Roast Beef, whose rambling speech is conveyed in a slightly smaller font with no commas.
Bob and George also uses this to lampshade, subvert, and Double SubvertContractual Immortality. The characters Bob and George can't die because their names are in the title of the comic. When the plot calls for their (temporary) death, the title of the comic temporarily changes in order to allow it to happen.
And when you have two parallel stories, running one on top and the other on the bottom, how do you find out what's happening in the top one from the bottom? Flight
In the V for Vendetta strip of Joe Loves Crappy Movies, Author Avatar Joe makes a snide comment about George W. Bush and is promptly taken into custody. He is then replaced by a government agent called George that replaces Joe for several strips, interacting with his friends and then girlfriend (now wife) Yeoh (who, strangely enough, are unfazed by this). Bringing this into Fourth Wall Painting territory is the fact that the strip's title changed to "George Loves Crappy Movies" and the movie reviews that accompanied each strip were made as if they were written by George (with his own Strawman Political bias).
Scenes set in the Ether are drawn more vibrantly, with no panel borders, and the art simply bleeds off the page. And on this page, Annie is in the Ether but interacting with the physical world; it's represented by her reaching into an inset panel. A god in the Ether is powerful enough to light up the panel borders.
After Rey's revelation in Chapter 31 that Annie indirectly caused Surmas's death., the panels and art become increasinglywavy to show Annie's fragile state of mind, which culminates in this page, in which Annie looses a wall of flame to cut off Eglamore as she runs across the bridge to Gillitie. The borders become warped and burnt, as if reacting to the fire.
After Antimony's traumatic meeting with her father, the art becomes sloppy and simplified during her Heroic B.S.O.D..
In the City Face filler pages, the Shout Box below the comic doesn't display reader comments—instead it shows comments from the Animated Actors involved in City Face, or other other characters in-story. These posts can no longer viewed in the comic archives, but they can be viewed here.
In 8-Bit Theater, after Thief's class change, he's seen in a red outfit for a few strips, then changes to black. When Black Mage asks him about it, he replies that his outfit was always black — and the red outfit in the archived strips was changed to match the "new" black one.
In addition, one of the many, many abilities of resident omnipotent jackass Sarda is a spell that lets the caster rewrite a person's speech bubbles to change what they just said to something Sarda finds more satisfactory. Something Sarda finds more satisfactory, as Black Mage finds out when he learns the spell and tries turning it on Sarda only to change the insulting remark Sarda just made to something more insulting.
In Lick My Jesus (which is, unfortunately, no longer accessible), one strip was based around the idea that different fonts were different languages. One character admitted, "I'm sorry... I don't speak Garamond."
Kinda like the old Brit ComAllo, Allo, in which different languages are represented by different accents — the Germans speak English with a German accent, the French speak English with a French accent, and so forth. One British character's "French" accent is very, very bad and leads to him saying things like "Gud moaning" rather than "Good morning".
In a similarly defunct example, This is, a webcomic presented as a series of brief, tongue-in-cheek descriptions, had as its 404 page a picture and brief, tongue-in-cheek description of a 404 page. Sadly, it has since been replaced by the 404 page from the author's subsequent project, which is significantly less meta about itself.
In Antihero for Hire, the eponymous Anti-Hero was kidnapped, resulting in an All Up to You situation. As a result, the comic's panel borders changed to white and pink, the rescuer's colors. Taken even further with green panels matching a comic relief character's scenes.
Schlock Mercenary used to use different fonts for the (English) speech of different races of beings in the galaxy. Humans "spoke" in a Courier-like font, the AI entity Petey spoke in a font that filled empty space inside of letters with a dot, and the F'sherl-Ganni aliens spoke in a very "pointy" font. The author phased out this practice due to the difficulty that fans had with reading these exotic fonts, but not without a fourth-wall-breaking strip to explain it. There are still a few holdouts, however - Ennesby and Schlock use different fonts from most other characters, since they use lowercase and most of the humans and other sophonts in the strip don't.
Another strip involved a character asking the narrator to move the narration box so she could see how bad a gunshot wound was on another character.
This page of Spanish webcomic ¡Eh, tío! allegedly depicts an epic zombie battle involving a ballpoint pen and two chickens — except that the image links for the middle six panels are deliberately broken. (Unfortunately Firefox 2 doesn't show that images are missing, so that part of the joke is lost to some.)
This page of the Spanish webcomic GeekInLove depicts the characters hunting a "archtypical" internet troll, but he is smarter than the main characters thought and he breaks the strip and goes down to the comments area to escape. He is still chased by one of the heroes, who finally kills him in the comment entry box. The "comment area" is in fact a mockup, but it's very well done and the comments are perfectly synchronized with the action.
Chapters 5-2 and 7 of City of Reality are brilliant examples. The introduction of the Choose Your Own Adventure Device in 5-2 is fairly straightforward, but you won't see the Chapter 7 example at all unless you read an offsite version of the chapter whose link is provided at the beginning.
This comic, by the author of City of Reality while not part of a continual series, is a wonderful, if creepy and somewhat depressing example of Painting The Medium.
Used occasionally in xkcd, such as in this strip, where speech balloons crossing the panel divisions are used to represent an interaction between present and future. Randall Munroe paints a nice Fourth Wall, and doesn't want to see it broken.
This strip of The Antagonist, where a counselor points out the eponymous ex-villain's, K's, specific speech, assuming the villain is immersed enough in the the act to be able to see his own word balloons, to which K answers, "This isn't a comic book."
Homestuck, like the other MS Paint Adventures stories, gives the readers the opportunity to influence what happens in the story by using the character specific suggestion boxes on the forums. However, after one character's house is hit by a meteor at the end of Act One, his suggestion box was locked, and replaced with a picture of a crater, until he was controllable again.
At the end of the fifth act, Doc Scratch takes over as a first-person narrator for a while. (All of the story up to this point has been in second person.) To make his text easier to read, he rewrites the site's CSS to have a green background. The top of the page is also replaced with a wide shot of his home (which actively changes as he and his guests move around in it.)
Space shots of the players' session shows the various planets (Skaia, Derse, Prospit, etc) with their orbits and neat descriptive labels. These appear to be more than mere subtitles, as a few shots show characters looking up from one planet or another at the giant 3-D letters hanging over their head. Given the nature of the game, it's entirely possible these labels really are there next to each planet.
During [S]: Cascade, one of Jack Noir's attacks rips the flash window larger. The effect is slightly less impressive on Newgrounds, because of their border.
There is also the practice of chat-users typing in their "quirks" (these quirks being different styles of typing; for example, Tavros rEVERSE CAPITALIZES while Vriska repl8es letters and sounds in phr8ses with 8s). While technically the quirks are literally being typed out by the trolls in their chat logs, they are still employed in their speech bubbles when they're portrayed talking face to face. The humans, trolls, and Cherubim are just speaking normally when they talk out loud; the quirks are only used to emphasize the differences in their mannerisms and personalities.
The Big Bad later changes the story's CSS in a similar manner to Doc Scratch, except instead of providing abridged narrations, he uses his narration to show his fan fiction. This later gets a flash sequence that switches between his location and the main story proper multiple times, and during that, everything (except for the dark green at the far ends of the page) flips around between the two layouts to show which part of the comic the flash is focused on.
In Zebra Girl, spiky speech bubbles signify that the speaker is a demon.
Girl Genius does this with speech balloons. Rectangles for machines, spikes for shouting, wavy edges for madness, dashes for whispers, icicles for hostility and icons for clank language. Afewexamples. Othar Trygvassen (Gentleman Adventurer!) uses a special font when announcing his name.
Flashbacks and memory recollections are denoted by sepia panel colours.
When Agatha's spark was supressed at the very beginning, the comic was coloured in harsh black and white. After the locket supressing it was stolen, colour began to return to the comic in decreasingly-washed-out shades until the comic was eventually in vibrant full colour.
The Fan WebcomicRoommates, and its Spin-OffGirls Next Door, does this a lot. Different characters' speech is written in different fonts, and various kinds of speech bubbles are used depending on character mood. (It's hardly possible but the Hungarian translation is actually worse in the weird font department... but it's consistent between the two, which the originals aren't.)
In The Mansion of E, each species has its own dialogue-font, and a few feature colored speech-balloons as well.
In Zelfia, males and females speak in different fonts.
One story arc in Leftover Soup had Ellen and then Jamie being introduced to Lily's new RPG setting, Florenovia. Since they heard it said out loud and didn't know how it was spelled, their speech balloons also misspelled it based on their respective guesses until they'd seen it written down.
Erfworld, has some artifacts that are computer rendered instead of drawn like everything else. This is to demonstrate how otherworldly they are.
Goblins has the Axe of Prissan shattering, releasing the Demon Lord's influence on the surrounding world. As it progresses the panel borders go from plain white to a diseased green with peaks of a hellish glow starting to appear. Then the ichor leaking from the Axe gets on the frame and starts webbing across it, spreading from the edges to actually cross the panel itself.
Planets and dwarf planets not only can't understand each other, they can't even hear each other. This is represented by planets speaking in Speech Bubbles and dwarf planets in Thought Captions.
Black Hole, who uses telepathy, has dialogue that appears directly onto the page with no word bubbles around it, is very large, is shown in a pixelated font, and usually has some kind of glitch effect around it.
Ceres, who Came Back Wrong and who might now just be an Empty Shell under Black Hole's control, has their dialogue/thoughts appear the same way Pluto's do, but as a garbled jumble of letters overlaying each other so thick that they're impossible to read.
The Disaster Masters from Cucumber Quest each have their own custom speech bubbles. Splashmaster's has water drops hanging from them, Noisemaster's is jagged (although they later turn into regular ones after he drops the "hype-man" persona), Mutemaster's are shaped like clouds, Rosemaster's has flower stems around them (that grow thorns when she gets angry) as well as the first letter of every speech bubble being in cursive (which get upgraded to a super fancy script when she's in her Crocus-powered giant mode), and Glitchmaster's are text boxes akin to old RPGs like EarthBound.
In Darths & Droids, strip titles are usually simple and/or witty, with an occasional Shout-Out. When Pete takes over the game in Episodes 333-353, their titles became more verbose and dscriptive of their contents, with a bit of self-gratification, as if Pete himself was writing the strip titles. Once the regular Game Master returns, the titles return to what they were like beforehand.