There are two relatively popular series I reaaallly cannot tolerate:

Yamato Nadeshiko Shichihenge
Gakuen Alice

I read reviews on both series and the general feedback was positive, but no matter how many attempts I make to get into either of these series, IMO, they are just awful

Basically, almost all the shoujos people already mentioned here (with a few exceptions).
But probably the ones, the popularity of which really surprises me are Kimi ni Todoke.
and Fruits Basket. Sooo booooring, I couldn't sit through a mere chapter. The same with the anime, I stopped watching them after like 5 mins of ep.1.

Kaichou wa maid sama definitely. I don't know why, but the moment I see that manga, I get very irritated. It's really cliched. Koukou debut too was okay, not that great. Same applies to Skip Beat.I also didn't understand the hype behing Hiruunaka no Ryusei.

Fushigi Yuugi definitely. Oh my goodness, Miaka is irritating af. She's just so immature and I didn't feel the character development. If there was, it would've been only a friggin' smidge. I'm currently reading it and I'm almost at the last volume. Ugh. It's torture. I'm only finishing this because I didn't want any loose ends and I'm almost done with it. I loved the animé when I was a kid.

W Juliet doesn't appeal to me, too. I dropped it when I reached 30+ chapters or so. Miura, the MC, wasn't as strong as I thought, mentally speaking. She was too dependent on Makoto. When something's wrong, the two often jump to conclusions and doesn't wait for the other to explain their part and will just make things worse--I got too tired of it and it was repetitive.

Well, those two, so far, are the shoujo mangas that pissed me off lol

I'm pretty sure I've answered something here before, but it's always fun to revisit old threads, then again ,there are always new series popping up that you may like or hate.
Anyway, someone above me mentioned Hana yori Dango and even though I've never read the manga, I did watch a bit of the Korean drama based off it. I didn't hate it, but it does have issues that I think were a little too glossed over.

I can't say I dislike some of the ones mentioned because the summaries are so unappealing that I don't even feel like reading them, like Skip Beat, High School Debut, etc.

This one was not maybe really popular, but I ended up not liking.It was Hoshi wa Utau.
I thought the protagonist was too much of a "nice" girl with a horrible past, and the romance was bleh,
It was a love at first sight that I wasn't too fond of.

YES TO EVERYTHING YOU SAID. *clap clap clap*

Late to the party but Kaichou wa Maid-sama for me. It baffles me how popular it is when there's barely any character development or plot. Dropped it after many, many attempts (due to its apparent popularity). Unfortunately, it seems most people like it simply because 'Usui is hot,' but that alone shouldn't warrant this much credit. At the end of the day, there really wasn't enough substance to keep my interest. I tried some other series by the same mangaka and I found that most of her characters tend to be more "wish-fulfillment" or cliche rather than 3-dimensional. I feel like I'm crazy for being the only one who seems to notice this.

Fruits Basket was an age old series everyone loved but I didn't. The rest of the story was fine and there were parts where the storytelling was beautiful, but every time I saw the MC I couldn't keep reading. No character is that saintly and unrealistic. However, despite not liking FB, I do see why it's regarded as a classic.

Secondarily but to a lesser extent, there are a few others that are purely slice of life that I can't seem to get into:
-Ao Haru Ride
-Hirunaka no Ryuusei
-Kimi ni Todoke
-Orange
-Say I Love You
-Bokura ga Ita
I'm curious, what's particular about these stories? They all seem to be the same predictable formula.

Ones I do like are Ouran High School Host Club, Vampire Knight, DNAngel, Ghost Hunt, Kurobara Alice, Special A, Full Moon wo Sagashite, Boku no Hatsukoi wa Kimi ni Sasagu, Momo, and La Corda D'Oro, to name a few. I guess I tend to like stories where romance is secondary to a larger theme or plot.

Thought Vampire Knight was pure trash. Zero was trash and Kaname was better.

I didn't like Orange for the longest time, but I finally changed my opinion of it. It's okay.

I tend to have problems getting into shoujos if the parents of the MC's stories are too over the top and are covered for too long. Like Marmalade Boy, the whole parent swap thing was weird. I love when the parents are likeable. Now, don't get me wrong, there are some over the top parent stories I have liked, it just depends on how it's done. I tend give a breath of relief if the parents barely show up or are dead.

I read maybe 10 chapters, but I just couldn't take Skip Beat! seriously. However, I'm currently reading the new arc to try and change my perspective about the series.
I could never finish Tokyo Crazy Paradise nor bring myself to continue the rest of the series. I just don't like it.
I started Vampire Knight and thought it was okay, but not the greatest work ever for me. Eventually, after certain events, I just dropped it because it was getting too hectic. Strangely enough, however, I kind of enjoy Vampire Knight Memories, though I mostly stay because of the relationship between Aidou and Wakaba. They are just too adorable!
There wasn't any real appeal for me at all when I read Dengeki Daisy. I stuck around for several chapters, but I couldn't bring myself to continue reading it. It just wasn't for me I guess. I've been considering giving it a second try, but I'm not sure if I'll ever get around to it.
And finally... Black Bird. I managed to read about half of the series because I wanted to find out how they would resolve the ultimate dilemma (that was the only reason I stayed so long), but ultimately, I gave up and only came back to see how the author would finish it up. It was rather off putting though, for the duration that I read this series, because of Kyo's character. He was just too obsessed with Misao and it felt rather unnatural.

Apparantly everybody I meet lately at some point adored Mahou Shoujo Madoka Magica and I just stood there like

________________
I think therefore I err.

I read all 4 major genres (shounen, seinen, shoujo, josei) and I'm a male in his 20s. I see it likes this, you can enjoy any of the genres, but don't expect them to cater to you if you aren't their demographic.

For me is sailor Moon never understood why vilains let peoples energy flow back.

I've been avoiding Skip beat like the plague and I've dropped Vampire Knight and Dengeki Daisy...so I feel you...I think at the time they were popular and thought I should try riding the hype and it didn't work out. I think I finished Black bird though...at the time i think I liked it

Kimi ni Todoke, though I still haven't really read it. From what I already know, and hear from the fans/spoilers, the story is reallyyyy slow and the misunderstandings are so cliche and annoying. I've been thinking of just reading the last few chapters.

Watashi ga Motete Dousunda is one that I did try to read and watch but I couldn't find the appeal. It was so cookie-cutter and the female lead was the typical one, but even more insufferable since she was a crazy fujoshi.