The author of Gunnerkrigg Court admitted that the second chapter doesn't fit with the rest of the comic, because he was still figuring things out. Since it's popular with the fans, he's left it in place.
One of the first plot arcs in Questionable Content involves an aborted romance between Marten and Faye's coworker Sarah. Sarah vanished completely within the first 50 strips, as Faye and Dora became the female leads.
XKCD initially wasn't even a webcomic, it was a site for Munroe to upload random sketches.
Keiki felt more like a Slice of Life comic in its early years, while the plotlines gradually became more outrageous.
Dan and Mab's Furry Adventures initially opened with it being quite clear that the characters were derived from the early MMO Furcadia, but then moved to being a more fleshed out world of its own, even if still retaining some of its old "MMO made real" elements — Alexis' Banhammer became a magical greathammer, the Twinks become a "normal" organized crime gang, etc. And there are also other elements that linger a while before being more or less phased out — for example, Lorenda was introduced having saved Jyrras from muggers by eating them, got evicted because she'd eaten her neighbors and then proceeds to eat several door-to-door salesmen. While she was admittedly self-proclaimed as preferring not to eat people, and this was a common source of friction with her mother, it hasn't been mentioned for hundreds of comics. In fact, neither has her much more predatory mother's tendency to eat people.
Breakpoint City begins with poor continuity, flimsy logic, dumb jokes, and not much plot. It has since developed story arcs, better continuity, better humor, and actual semi-plausible (considering the Time Travel, aliens, and what not) logic.
Penny and Aggie was originally pitched to Newspaper Comic syndicates, and early installments reflect this. There's much less sense of the passage of time; character development ranges from slow to absent; the pets Charles and Finister are featured much more often; details about the setting are purposefully obscured to the point that the series could have taken place in Canada, and the Les Yay, aside from one bit of Love Letter Lunacy, is basically absent, even Sara in one strip being noticeably attracted to a boy; the Retcon of this makes it a plot point.
The earliest comics had copious Fourth Wall Breaking, little or no backgrounds, poor story arc planning (some of which still poses a problem), and Tedd not having a permanently visible mouth.
Quite a few characters ended up being subjected to Characterization Marching On compared to their previous personalities. Elliot was just as much of a pervert as Tedd (he's now incapable of even thinking dirty thoughts while trying to), Tedd was more a straight pervert instead of a Chivalrous Pervert, Grace was aware of the sexual implications of wearing nothing but a trench coat (where afterwards she suddenly became the Innocent Fanservice Girl with No Nudity Taboo) and Sarah was much more of a feminist (before the feminist part was shifted over to her friend Susan).
When the "Elliot gets turned into a girl" arc was first published, Sarah and Susan both seemed cheerfully willing to make out with her if she was interested. Though there was a justification (pheromones), the author eventually realized the Unfortunate Implications of the whole thing, so a few lines and panels were quietly changed.
Schlock Mercenary introduces several pieces of hardware as new or exceptional, then pretends that they were normal all along. The captain needs to be told what a fabricator ("Fabber") is, but later we see that they're widespread, important and something Tagon should probably know about. Even more odd is the fact the mercenary company doesn't start out wearing armor, either low or high profile, until they encounter a unit wearing some.
And then there was the copious Fourth-Wall Breaking, with the narrator frequently getting pulled into the action. The last time the Fourth Wall got broke was in 2006, with the author making a personal appearance during a near-death dream-sequence - one is forced to assume that they finally had that wall reinforced with fullerene armor, or possibly some nice hullplates...
Also, the 'Grunts' used to be so stupid they could barely talk without resorting to Hulk Speak. Nick couldn't count past 7 because he lost 3 fingers on one hand during an accident. While they're still not exactly brilliant - with Nick in particular being prone to not understanding figures of speech or long, complicated words - they've at least reached the point where they're BELIEVEABLY stupid.
The first month of Homestuck consisted of John hanging around in his room and house and getting nothing done, and that was followed by a few months of mucking around with Sburb's ability to let them them to build and manipulate objects in each other's houses. Then things get more intense, to say the least. This can be chalked up to the fact that at that point, Homestuck was still driven by reader commands and they'd just come off the tail of the incredibly silly Problem Sleuth, so this is what people knew to do; the suggestion boxes were closed partway through and that's when the series is generally considered to have grown its very strange beard. A common symptom of this is people finding it difficult to get into Homestuck because of how long the first few months of hanging around is (though said first few months includes loads of Foreshadowing, Chekhovs Guns, and subtle set-ups if you know where to look).
The beginning of the first Act has a moment where the player directly interacts with the game world and moves an object on John's behalf. This never happens again in the comic and for the most part if a character wants to do something they just do it themselves.
When the trolls are first introduced, Karkat makes comments such as "quit playing a girl's game", or making fun of Sollux by implying he's never had any relationships with a girl. Lines like this were written before Andrew Hussie decided upon a lot of the World Building for the trolls (namely that gender is arbitrary to them).
One of the first strips in Webcomic/Misfile has Emily flipping the bird. Later strips show that she is not the sort of person to do that.
The first 13 comics of The Order of the Stick have no plot and take place in a blank featureless dungeon. Then they introduce the Excuse Plot of having to kill an evil lich. Around the 120th strip they finally get out of the dungeon, but there still isn't much emphasis on plot. Around page 300 however, things start to heat up...
Even outside of Cerebus Syndrome and the Genre Shift, early Wapsi Square still had narration, which was absent from later strips as well as characterization that differed from what would come later.
The initial focus of Neglected Mario Characters actually wasn't comics, but instead humorous biographies and fact sheets for various obscure Mario characters. Then Jay Resop created a comic based on the end of Super Mario Bros. 3, and from there the site gradually changed...
Sire starts before the main character receives her distinctive facial scar. The cover of the first chapter stands out as it's used in all the banners and promotional material and does not feature the scar.
User Friendly had a long list of cast members we've never seen or heard from again in its first year or two, including a few female staffers, with Miranda being a standout as the only female tech, not the only female in the company at all. Pitr doesn't speak with a Slavic accent, Sid is not there at all, and the Chief's hair has to be seen to be believed.
Zebra Girl started with very random magical hijinks and lots of postmodernist jokes that made absolutely no sense and were only funny because of how unexpected, and out of place they were, even during its first serious story arc.
Early Goblins strips often involved back and forth interaction between the adventurers and their oversensitive DM. As the series went on, that was increasingly dropped in favor of more internally consistent worldbuilding and character interaction.
Bob and George: in the early stages, the Mega Man jokes were only there to fill in until a hand-drawn strip could be introduced, but after a couple of false starts, the hand-drawn part was dropped entirely and it was retooled into a full-time Mega Man sprite comic. There was also character-related oddness such as Bass having a decent IQ (later he became The Ditz even by comparison to Mega Man).
Looking for Group got its start as a straight-up World of Warcraft parody. It was much more cartoonish in both drawing style and narrative, with Richard burning Kale to ash in his first appearance, then having a conversation with him as a pile of ashes in a pouch while seeking out the priestess Ben'Joon ("Benny") to resurrect him. In the years that followed, the comic has developed its own unique world. It remains comedic but has lost its more cartoonish elements.
Brawl in the Family had a much cruder art style, and largely revolved around jokes about Kirby eating random things rather than the deeper plot lines and characterization in later issues. The comic also initially included quite a few Take Thats (such as one directed at Electronic Arts), in contrast to the later strips mostly avoiding potentially controversial topics for the sake of concentrating on the comic's signature cute, universally humorous gags.
Achewood's early installments are virtually unrecognisable. Strips tended to rely on non-sequitur humour. Mr Bear wasn't the elderly sophisticate he would be established as later on. Philippe was described as "retarded" rather than simply being 5 years old. Characters like Pat and Lie Bot were far more prominent, the former being more of a beatnik. Ray and Roast Beef were minor characters, the former established as being quite poor. The fact that Philippe, Teador, Lyle and Mr Bear were stuffed animals was a major recurring element. Basically, pretty much everything apart from the characters' names was retconned out.
In Educomix, the characters all speak strangely, but only slightly, and some more recent strips only have dialogue that would make sense in real life. However, the first few strips contained some of the strangest dialogue, e.g.:
Dave: I would like to apply for a job descriptions of the fire engine, ma'am.
Also, the first four strips used a different font to the one which became standard in strips 5-200.
Sunstone used to be a collection of pin-up images consisting of Ally dominating Lisa and Anne. Many of these featured descriptions of Ally enslaving them and subjecting them to unsafe punishments, as might be expected of a pure fantasy scenario. Since deciding to write Sunstone as a serious story aiming at debunking popular misconceptions of BDSM the author removed most of the problematic strips...
morphE is a unique example. It is entirely coded and developed in Flash and it is painfully obvious that the creator's ambition out-reaches their abilities in the first 60 or so pages, particularly with the jerky "fighting" animations. Compare this offering to this recent animation.
At the start of The Whiteboard, the Petting Zoo People main cast was treated as something unusual in a human world. The author soon dropped the "something unusual" angle as not really being where he wanted to take the webcomic, and since then has gravitated over time towards making more of the characters anthropomorphic animals.
Erfworld is pretty good at keeping up with its own continuity, and holds well together if read from the beginning. However, the original cast page at giantitp.com, before it moved to its own website, was posted before the first page of the actual comic, and there are some minor deviations from later continuity. In particular, "Dirtamancer" is spelled "Dirtomancer", and the cast page refers to the Plaid and Croatan "tribes", not mentioned in the comic itself, instead of aligning the characters with "sides", which are typically named after their capital cities. (In fact, the prequel book reveals that Wanda was popped in the Goodminton side, making no mention of the Croatan tribe.
And in the actual comic, the first uncroaked units to appear are three skeletons. After that, all uncroaked units are portrayed as decaying zombies.