These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Ass Pull: Arguably the ending, which to some people had absolutely zero foreshadowing and came out of nowhere to fix everything.But when you rewatch, there are hints in everything from small gags like Sanae's and Akio's "new names" for Tomoya to more important things like Nagisa's script to, oh, Kotomi's and Yukine's entire arcs.
Better on DVD: The anime series has a lot of tight arcs and complex foreshadowing, making it the LOST of anime. On the other hand, some fans feel that the abundance of Tear Jerkers, especially in ~After Story~, makes it too emotionally overwhelming to watch in one sitting.
The English dub, in stark contrast to the dubs of Air and Kanon from the same dubbing studio, which are highly praised (especially Kanon). Complaints boil down to two areas: Mispronunciation or mis-stressing of names, and Kyou's voice actress sounds too old. Oddly enough, very few complained about the quality of the acting itself.
The fact that Clannad's dub was handled by Steven Foster (who is absolutely despised by a vocal minority of the fandom) as opposed to Kyle Jones (who directed Air and Kanon) undoubtedly played a huge role in why criticisms of this dub tend to stick. However, the earlier dubs also mispronounced some names and had the occasional questionable casting choice, yet they're justifiably well-regarded.
There's no doubt that this dub (due to Sentai having No Budget) was not given the level of care the earlier ADV dubs got, but it still compares reasonably well to its predecessors, largely due to being made up almost entirely of veteran voice actors – as opposed to Sentai's later efforts, which use mainly new talent (since most of the longtime Houston talent have decamped for greener pastures).
Tomoyo. She even gets the sequel visual novel, Tomoyo After. Especially when in the anime, before the Bonus Episode, she's one of the characters who doesn't get her arc completed properly.
The same could be certainly said for Kyou, who now has the same status as Tomoyo in the fandom – incomplete arc becomes an OVA.
Sunohara also qualifies as an ensemble darkhorse due to his large popularity with the fanbase. Apparently the only place where he has little to no fans is among his creators themselves; even though he has haters or people who finds him to be of little importance, you better believe that are many image boards that hate everything about Clannad, except for Sunohara.
Akio is popular because he's such a big kid at heart.
Even Better Sequel: As good as the first season was, After Story managed to top it, being considered one of the best anime shows of all time by a wide margin.
Fandom Rivalry: Quite a bit with the Toradora! fandom as to which is more emotional, and which is a better romantic comedy/drama in general. This one seems a bit one-sided, as CLANNAD fans generally enjoy Toradora! as well.
Faux Symbolism: Tons of it. For example, the hill Tomoya and Nagisa climb up together represents life. The fact that they climb it together means that they journey through life together.
Fridge Horror: There is a theory about the ending, saying that time did not turn back to save Nagisa and Ushio, but rather that an alternate universe was created where they lived. This is all well and good... until you realize that the universe where Nagisa, Ushio, and Tomoya are still dead.
Germans Love David Hasselhoff: The anime series seems to have a sizable Latin American following. English-speaking anime fans also consider the series a masterpiece.
Growing the Beard: There's a reason ~After Story~ gets consistently better reviews than season one — and it's not because of the first quarter of the season, which is more or less just a continuation of the first season. Then a whole series of Wham Episodes simultaneously push the time frame into fast forward while pushing the material itself into darker and darker thematic territory – without losing its sense of humor.
Harsher in Hindsight: You know that thing about Sunohara barely showing up in After Story, even though he's meant to be Tomoya's best friend? Gets a lot sadder if you've played Mei's route in the visual novel, in which Sunohara claims that he and Tomoya are close enough that they'd definitely stay friends after they graduate. Guess Tomoya was right to be skeptical, after all.
Sunohara: The friend I have right now is not related to me just by the school. Even if we graduate and more far away... Even so, when we have holidays we'll come and meet... That kind of relationship.
Tomoya: Sorry, but far? Really? [...]
Mei: From now until you become an adult... Even if your surroundings change... You guys will still be friends, right?
(Visual Novel) Kappei with both Tomoya and Sunohara, having Ambiguous Gender. Sunohara, in denial, still pursues what Tomoya calls "unrequited love." Tomoya was just confused on Kappei's gender at first but he was never actually interested, Sunohara on the other hand... Though if Kappei really had been a girl, he/she would had undoubtedly be part of Tomoya's romantic harem.
Played straight in the "Bad End" or "Sunohara route." In the end though, the "route" is just making fun of the fact that Tomoya made all the girls fall for him but rejects all of them; he just isn't interested in girls. Though his rejections were subtle, you still feel bad watching the girls' reactions.
HSQ: Very high in the second half of ~After Story~.
Iron Woobie: Sanae. She only cries for her daughter five years after her death. The scene where it happens is really heart-wrenching.
The "misunderstanding" between Ryou and Nagisa on the rooftop. In one scene Kyou also appears to like Kotomi a lot, leading to the famous Glomp. The troll subs don't help either.
On a more serious note, Rie Nishina and Sugisaka from the music club. Sugisaka is very protective of Nishina, they're holding hands in the After Story credits, and they're apparently living together in the Grand Finale. It's possible they were meant to be a downplayed version of the Token Yuri Girls trope.
Mary Sue: Tomoyo could be considered this, in fact, sometimes her qualities go beyond that of a typical Manic Pixie Dream Girl. This is especially pronounced in her Alternate Universe episode where the writers didn't know how to create drama for a character as flawless as her and just decided to force a break-up between her and Tomoya.
Memetic Molester: A small example, but Tomoyo with her bear costume is often associated with the pedobear by the fans.
Moe: Good lord. Every female character in the franchise. For instance, Nagisa, Fuko and Tomoyo all made it to the Top 8 (quarterfinals) in Saimoe 2008, and Nagisa even made it to the Top 4 (semi-finals) that year, before losing out to Kagami from Lucky Star.
The line "I can no longer play basketball" and its delivery, not to mention Nagisa's reaction, initially seems incredibly awkward and melodramatic. It's only when things are given more explanation that things seem more reasonable.
Late in Fūko's storyline of the game, Tomoya and Nagisa come up with a plan to see if Fūko, who thus far appears to be a spiritual projection from her comatose, in hospital body, can be seen by her elder sister; something she was very uncertain about and required great assurance from her friends it would work. The plan is interrupted, brutally, as when Nagisa brings Fūko out in front of the elder sister whom Tomoya is chatting with at the festival, the sister comments almost nonchalantly to Tomoya, and in front of Nagisa and looking straight through Fūko, 'That girl stopped breathing yesterday.'.
Nagisa's death, no matter how you look at it, was meant to be this in every aspect. After all the Character Development she went through, no doubt because of Tomoya's presence with her, we're then reawakened to the fact that, even if she's a strong person, she's still physically weak. When she insists on home delivery, the alarms were already being raised, and when we find out that a heavy snowstorm occurs on the day she gives birth, it's really no surprise that she was going to die anyway. And yet, knowing this, it's still a Player Punch.
Rescued from the Scrappy Heap: Nagisa initially was downright despised by many militant Kyou/Ryou/Kotomi/Tomoyo fans who simply could not accept Nagisa and Tomoya as the Official Couple. However, during and after ~After Story~'s run, Nagisa became a much more respected character even among most of those hardcore anti-Nagisa shippers.
Shipping: Fanfic writers have taken the series' stance on multiple universes and ran with it, having romantic pairings in every conceivable configuration.
The 2006 Toei Animation movie can be unintentionally hilarious to someone who's already seen the KyoAni series.
The English dub of the series, for those accustomed to the subbed version.
Subbing vs. Dubbing: Clannad was picked up by Sentai Filmworks, the heavily-stripped-down (meaning they had No Budget to work with) successor to ADV Films. Due to this show being Sentai's very first post-resurrection license, it was initially released Stateside subtitled-only, despite earlier promising a release similar to Kanon's. Sales were strong enough to justify going back and adding a dub when the Blu-Ray version came out a couple years later. However, the dub received mixed reviews from the hardcore fanbase who had already seen the Japanese.
Tear Jerker: Along with basically the entirety of Key's works, Clannad pretty much defines this trope by forcing a Break the Cutie moment on virtually every character and reducing every fan to complete sobbing wrecks by the end of the series. To say this series is sad is, well, pretty accurate, though to be fair it does have equally heartwarming moments which will also reduce you to a sobbing wreck.
They Just Didn't Care: Happens occasionally in the dub. While your mileage may vary regarding the casting of the actors, names do get mispronounced or mis-stressed. Also, there are several scenes where there's a joke that involves Japanese characters onscreen. The translation used in the dub is an extremely straight one that did not adapt the more culturally-specific jokes or puns.
Values Dissonance: The disrespect and avoidance Tomoya shows his neglectful father comes off worse in the original Japanese, though other audiences may find it justified.
Video Game Movies Suck: Massively averted with the anime series, which is regarded as one of the highlights of the late-2000's. Played straight with the movie, as it's not nearly as well-regarded as the series. Shame, considering that movie is the last directorial effort of the late Osamu Dezaki.
What an Idiot: Pretty much everything Sunohara does toward Tomoyo. Or anything Sunohara does, really.
Tomoya. First, he lost his mother, then became estranged from and abused by his father, rendering him unable to play basketball, and thus probably losing the only dream he ever had. Later, he loses his wife, and becomes estranged from his own daughter. Five years later, they reconcile, but after a few months, the daughter falls ill and dies. Tomoya then dies from despair. He got better, thankfully.
Which, according to this◊, lets the original timeline go to pot when you consider the horrible possibility that in at least one universe, Nagisa and Ushio were able to meet in the afterlife after they died but would never see Tomoya again; he was effectively erased from that timeline due to being sent back in time to the Illusionary World after he died, a la The Legend of Zelda: Ocarina of Time's Link, only more depressing. Considering this show's view on multiple parallel worlds, this is hardly a farfetched idea.
Kotomi in particular too. Losing her parents as a child, bearing adult responsibility at that age, and never developing social skills, thus no friends, makes for an incredibly hard childhood. Poor girl just needed someone to give her a hug, too. Other than the deaths of Nagisa and Ushio, she had it just as bad as Tomoya. Not to mention the way she's visibly shaking and asking whether the other girls are going to bully her when Tomoya tries to get her some friends. You want to give the poor girl a hug.
Ushio. She never knows her mother due to her dying in childbirth, then her father leaves her in the care of Akio and Sanae. Ushio and Tomoya finally reconnect, only for her to die of the same illness that affected Nagisa in the bad ending.