There was once a time where every anime fan had to have at least seen one episode of InuYasha. Every con would at least have a dozen people cosplaying as the title character. Hell, it occasionally leaked out of the anime fandom and it wouldn't be uncommon to see people on the street wearing merchandise from the show. Nowadays, the show's largely considered a joke that most newcomers would never dare to touch. This is likely because of the frustration amongst fans of the anime watching it for years only to see it end without any conclusion to any of the plot. By the time a conclusion was reached with The Final Act, the damage had been done, causing lots of fans to simply tell newcomers "not to bother with it" or "read the manga instead".
The fact that it became infamous for its atrociousFan Dumb (to the point where it was often used as the example for how obnoxious anime fandoms can get, at least before the Hetalia and Naruto fandoms came along) probably helped it reach this status as well, as more and more people were turned off of it because of the rabid squealing fan-girls and boys.
The original Fullmetal Alchemist anime was once hailed as an absolute masterpiece the likes of which the west had never seen (even gaining a lot of mainstream popularity with those who otherwise weren't anime fans). However, the anime going its own route created a rift between the manga and anime fans: the manga fans who found the anime lacking, and the anime fans, many of whom were introduced to anime by this adaptation. It's initial popularity was also helped by the fact that it came out at the time of the anime craze in the early 2000s, but for anime fans who were anime fans before that time, many felt as though the anime was being shoved down their throats. If Inuyasha was the Naruto of the time period then the first FMA anime adaptation was the Bleach. And for new anime fans who came after the early 2000 anime craze didn't have any attachment to the 2003 anime, and so would watch both anime side by side and found the 2003 adaptation lacking. Critics were split and it's fairly easy to tell whether the reviews were positive or negative based on whether or not the critic in question was a fan of the 2003 adaptation or not. If the reviewer is a fan of the 2003 adaptation then they will most likely give a negative review (often through Jade-Colored Glasses), however if they aren't then the review will be positive. Nowadays, you're just unlikely to find them among the FMA fandom unless you really dig, and even in the general anime communities they're very quiet.
Part of the reason for the heavy backlash the 2003 anime suffered was its sequel movieThe Conqueror of Shamballa which was rather poorly received as it more or less turned the whole show into a Shaggy Dog Story. It was around this time that people who wanted more FMA gravitated toward the manga and subsequently latched on to the Brotherhood version when it debuted in 2009.
There is also the fact that at the time the 2009 adaptation was announced there was a massive Hype Backlash by the 2003 anime fans, who saw no reason for Brotherhood to exist. However, by the time Brotherhood neared its halfway mark they reversed places with fans actually liking Brotherhood, while the 2003 adaption receiving Hype Backlash which resulted in it becoming Deader Than Disco.
Bleach started off as an overnight sensation, gaining rapid popularity in Japan (and in the anime fandom in the West) to the point of being considered one of the "Big 3" of Japan along with One Piece and Naruto. Around the time of the Arrancar arc however, Bleach suffered massive Hype Backlash due in part to its rather infamous reputation for Arc Fatigue, along with many controversial plot twists. Said Arc Fatigue also negatively impacted the anime, as well causing (multiple) lengthy filler arcs. To add insult to injury, declining ratings would lead the anime to be unceremoniously cancelled and replaced by a Naruto spinoff. These days, it's still fairly popular in English-speaking areas, but the fanbase is nowhere near as big as it used to be.
When Digimon Adventure 02 initially aired in the United States it was very popular,perhaps even more so than its predecessor, though there were criticism laid at the controversial epilogue. Now however, through it has a fair share of fans, it has become one of the most controversial and polarizing seasons of Digimon and is widely derided in many fan circles, especially on 4chan's /a/ board. The reason? Because an inversion of Vindicated by History happened and people saw that the epilogue was not the only part of the series with problems, but also due to a large number of plotholes along with a large number of plotlines that were either abandoned (ie: The Dark Ocean Arc and the Daemon Corps arc), or hyped up but rendered into irrelevance a while later(ie: the Destiny Stones Arc), along with a preceived "excess" of filler episodes making up the series, the rumor that the show ruined the Adventure universe in Japan and is the reason why every Digimon series is set in a different continuity and the fact that the series in the original language, after seeing the subs, was even more contrived than in the dub, it dosen't help that the series after that, through being somewhat divisive in the start, is now considered one of the best Digimon series in the franchise. Nowadays, talking about 02 would draw a lot of divisive Love It or Hate It responses, with the best season either considered Seasons 1 or 3 , through you certainly won't find many fans of Season 7.
However, there were several factors that led to this type of dub's decline. First, there was the controversy raised by several of 4Kids' later dubs. Namely, the violence in later episodes of Shaman King caused protests from offended parents, which led to 4Kids taking their practices to extremes for their dubs of One Piece and Tokyo Mew Mew; effectively stripping them of anything remotely Japanese. The creators of both series, not amused, thereby pulled the rights from them on the grounds that they made mockeries of their series. Second, the popularity of the films of Studio Ghibli, which enacted a "no-cuts" policy for studios that dub their films for foreign markets, proved that anime doesn't have to be toned down for audiences to appreciate it. Third, the rise of YouTube and other video-sharing sites helped uncut versions and subtitled versions of anime become more widespread, thus eliminating the need for sanitized dubs being the primary introduction to other types of anime. Lastly, this type of translation, as noted on its trope page, is expensive, much more so than a straightforward dub, and with fans having access to the unedited Japanese subtitles, there just wasn't a market any longer for heavily edited dubs as the 2000s wore on. As a result, the Cut-and-Paste Translation has largely been discredited as a dubbing practice. As for 4Kids, the license to Pokémon was moved in-house to The Pokémon Company International, and they continued to dub anime in this manner amidst years of losing money and being the subject of mockery from personalities such as LittleKuriboh and MarzGurl until the company was absorbed into Saban Brands in 2012; with the Yu-Gi-Oh! license being given to Konami.
TV anime adaptations of shoujo manga seem to be heading this way. Nowadays, most of them get adaptations in film, live action drama, or short OVAS. A lot of this probably has to do with anime becoming more male otaku-oriented, and the fact that shoujo manga itself (or at least the kind adaptable into animation) seems to be in danger of becoming this because of its Dork Age.
Haruhi in particular is notable because of just how quickly this can happen. As far as the Western fandom was concerned, the show debuted in 2006 to raving reviews and acceptance. The lack of a second season quickly succeeding the first turned the show into something like the Half-Life of the fandom, with constant anticipation and speculation with great demand for the series. The airing of the first episode in 2009 was met with exuberance. Finally, the rest of the novels would be animated! This great series will go on! Then the "Endless Eight" story arc happened, and in a matter of weeks the entire perception of the brand had been shattered. Fans were dismayed by the arc, while more casual viewers who had enjoyed the first season quickly found themselves wanting to have nothing to do with it. Suddenly criticisms started to extend from the mishap or an arc adaptation to the series as a whole. Being a major fan of the series in some circles went from being completely normal to almost something of a badge of shame. While reaction cooled in the coming months and the animated adaptation redeemed itself in the eyes of fans with the release of Disappearance in 2010, the fervor for the series by and large disappeared. From top of the world to bottom of the barrel in the span of three years.
CLAMP seems to be becoming this due to the lukewarm to almost negative reception of their more recent works and people becoming more aware and critical of flaws even in their older ones (such as overuse of Author Appeal, pretentiousness, and lackluster endings). Nowadays, they are simply remembered for their brilliantshojostoriesthat were created decades ago, not the obscure series they are currently making now.
Chobits is this especially. Once one of their most popular works, it's now only brought up in discussions about its writing problems and loads of Unfortunate Implications. There's a good chance people cosplaying its main character don't even know where she's from.
Usagi Drop was a very well-regarded manga with heaps of critical praise and a successful anime adaptation. Then came the ending and Rin and Daikichi got very squickily Strangled by the Red String for no reason other than apparent Author Appeal and the whole story was all about Wife Husbandry and nothing else. Cue nearly everyone dropping it like a hot potato and pretending that only the anime (which ignores the controversial time skip and glosses over the unsavory elements) exists. Even the American publisher seems to be treating it as an Old Shame.
While it still has a relatively small fanbase, Air has lost popularity, especially due to Angst Aversion and It Was His Sled. Those who would rather watch a fun action show will think twice before watching it. Nowadays, those who haven't seen the show have most likely had Misuzu's death spoiled for them, even on this very wiki.
Tokyopop used to be the English-language manga publisher up until its 2011 closure. Now it's mostly remembered for its mediocre translations and the incompetence of its CEO Stuart Levy. Also its contribution to the brief trend of awful, low-quality OEL manga did not help at all (in fact their over-hyping and focus on their unpopular collaborative project Princess Ai is often believed to be one of the things that led to their eventual downfall)
Mermaid Melody Pichi Pichi Pitch is pretty much this in the English-language magical girl fandom. A lot of this simply has to do with its target audience outgrowing it and it lacking anything to make it appealing to other demographics. It's now seen as Snark Bait and pretty much nothing else.
Ore Imo is another example of how quickly this trope can happen. Once a very popular light novel/anime, it's now known for its terrible ending and for giving birth to the creepy "imouto" genre.
While the Hetalia franchise as a whole is still fairly popular (though its fanbase is starting to dwindle for various reasons), the anime by Studio DEEN seems to be heading this way, as more fans are critical of its low quality and changes to the source material. A fifth season made a few years later greatly increased the writing and animation quality, but it apparently didn't perform well enough to get the series started up again.
Sites like Crunchyroll seem to have fansubs heading this way, as they can offer subbed versions of shows on the other side of the Pacific as soon as they hit the airwaves in Japan. On the other hand, some fansubbers feel they do a better job than the "official" subbers.
They are also still popular with the Bit Torrent crowd due to their accessibility.
Shugo Chara! was once theMagical Girl anime about 5 years ago, was a borderline Cash Cow Franchise in Japan, and received lots of praise from both viewers and reviewers. Now it's pretty much obscure. A lot of it has to do with the manga's lackluster final chapters, and the third season bombing so badly it killed off most interest in the franchise. Also many fans were starting to get tired of and squicked out by its Love TriangleRomantic Plot Tumor. The franchise still has a few fans, but they see it as a Guilty Pleasure now and little more.
Vampire Knight was once one of the few shojo romance franchises to get mainstream popularity, and is often credited for helping get more people into manga. Now thanks to its Seasonal Rot and large amount of writing problems later on it's now almost completely forgotten. It also became a near-Creator Killer for its mangaka.
Hot Gimmick used to be one of Viz's most popular shoujo titles, and was even one of its fist series to get a Viz-Big edition. Now thanks to severe backlash against Bastard Boyfriend manga the series is pretty much unknown, and saying you're a fan will get you very dirty looks in some circles.
Non-ironic Magical Girl shows aimed at young girls. The only examples still running and successful are shows in the Pretty Cure franchise, and even those have some parody/post modernist elements to them.
The Slayers anime is now pretty much forgotten due to Seinfeld Is Unfunny and the revival seasons bombing. It used to be huge in the mid-to-late 90's, but now good luck finding anyone who still remembers and actively watches it.
While it still has a handful of diehard fans, Naruto is pretty much dead in the eyes of the mainstream western otaku community, mostly due to Seasonal Rot and some Hype Backlash.