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.
Designated Protagonist Syndrome: Shirou lacks any real traits other than justice, doing good and avenging his losses. His lack of any real traits, however, is actually deconstructed, albeit whether it was intentional isn't clear; it's a result of the fact that he's a borderline Empty Shell and lost any sense of self and identity in the fire and is essentially dead inside. He defines himself and his self-worth by the heroic ideals he got from Kiritsugu, and clung to them in order to have something to live for.
Draco in Leather Pants - Gilgamesh can sometimes fall into this, with the fanon portrayals of him that tone down his Jerkass qualities considerably and put him into a much more positive light, in addition to some who ignore that he quite frankly wants to rape Saber, doesn't care about her consent and seems to even prefer her resistance. At times, his Attempted Rape of Saber is explained away by being purely attempted and not being something that succeeded, yet despite that, Shinji is strung up by the fandom for the same action. note Of course, he is (quite rightly) strung up not just for that particular attempt but for his other actions, including successful rape; but this comparison does apply. One must note that in both the original myth and the game Enkidu originally fought him due to him invoking Droit de seigneur, or the lord's right to a bride's virginity, where the consent of the woman didn't matter, and Values Dissonance can't be invoked with this because even in the original myth people thought he was going too far.
Ensemble Dark Horse: Lancer, who really gets The Worf Effect very hard in the series, but his wit, amiable and likable personality, and interest in fighting compared to the more goal oriented and ambitious Servants made him easily one of the most popular Servants. His glorious sendoff in Unlimited Bladeworks with killing Kirei after the latter ordered him to commit suicide is very satisfying as well.
Among the Servants, there's also Rider and Archer, although both are more important in the Visual Novel than in the anime; the latter is easily one of the most popular characters in the series, among anime-only and visual novel fans both. Gilgamesh also counts considering he´s considered one of the faces of the entire franchise despite having a somewhat minor role in Stay Night compared to Fate Zero.
Among the Masters, there's Ilya - like Archer and Rider, she's more significant that she appears, yet her compelling backstory and unique character compared to the rest of the cast makes her stand out.
The "I am the bone of my sword" invocation/chant for the Unlimited Blade Worksreality marble isn't given much weight or attention, and only seems to be there for the Rule Of Cool. Until the Heaven's Feel route, that is, where its meaning becomes painfully clear after Shirou uses Archer's arm for projection, catapulting him past his limits and resulting in an eventual rebound that reforges his body into thousands of swords, killing him from the inside out."I am the bone of my sword" indeed. At one point in Unlimited Blade Works, Archer tells Shiro and Saber that he lost his arm the first time he used a projection, which seems to be a lie as Shirou is able to perform projection and still manages to keep both arms throughout both Fate and UBW. But then in Heaven's Feel, Shirou has one of his arms blown off. Archer voluntarily has one of his arms grafted to Shirou, and "losing his arm" at this point enables Shirou to perform Projection for the first time not long after.
Also, Sakura's jealousy. Cute? A funny little argument with Rider about Shirou finding her attractive? Not so much after killing Shinji, going berserk and hitting you with the worst bad ends of the game plus her Villainous Breakdown against Tohsaka at the end, where it's also revealed that no, Sakura did not pick up the little cues that Tohsaka really did care about her all along.
Remember the humorous scenes you can get if you nag Saber for "a super move that can defeat a Servant" during training? In one ending of Heaven's Feel, Shirou actually wins against Saber Alter... by using Archer's super move with Kanshou and Bakuya against her. Though maybe it's just Hilarious in Hindsight, since that ending is actually really, really awesome.
In the Fate route, Rin half-jokingly speculates that Archer must have been a skirt chaser back when he was alive. Then comes UBW and we discover who he is. Suffice to say, he didn't chase skirts as much as he was chased by skirts.
GARnote Came from a post on 4Chan where someone remarked that he was "gay for Archer" because of his badassery, only to misspell it as "GAR" instead, and it took off from there.
Mis-blamed - As noted in the Complete Materials, Nasu didn't actually write the infamously bad sex scenes in this or any other Type-Moon game. Hasn't stopped 'Nasu can't write sex' from approaching Memetic Mutation levels - that may, admittedly, be true, but we can't say for sure without any evidence.
Moe - Sakura and Ilya stand out as the most notable cases, although Saber and Rin have their moments.
Shinji starts out as a Jerkass, but crosses the line fairly early by trying to kill off the entire school to power up his servant, and we find out in Heaven's Feel that he's raped his sister many, many times before the story begins.
Sakura does not cross this, despite killing and devouring hundreds of people, because she does so entirely subconsciously and is unaware that she is doing it. However, when her dark side rapes Rin in the last Bad End, even Shirou (who has sacrificed everything for her) realises that she's too far gone to be saved.
Dark Sakura in Fate/unlimited codes crosses this by keeping Bazet alive just so she can watch her suffer.
Even if Gilgamesh was helping the Big Bad in Fate, he crosses this in Unlimited Blade Works by ripping out Ilya's heart, to say nothing of how he got to that point.
And even before that, in the Fate route his description of what he's going to do to Saber when he defeats her is pretty sickening.
MST3K Mantra - This is essential for any of the hardcore fans who are addicted to the intricacies of canon to enjoy the movie at all. Never mind the complete excising of Shirou and Rin's opposition, for instance, just focus on the epic action scenes.
One True Threesome - There are two, Shirou/Saber/Rin and Shirou/Sakura/Rider. First is played straight by Unlimited Blade Works route and completely fulfilled in Good End of this route. Second is slightly hinted in Heaven's Feel route. Both are expanded at various levels in Fate/Hollow Ataraxia and many other associated works or materials and very popular in fandom.
The Good Times Montage and the music that accompanies that particular scene makes it hurt even more. Way to twist the knife there, Nasu.
In UBW, Ilya's death might not have carried as much weight were it not for the fact that you have to play through Fate first (where you befriend her), and watch a particularly heart-rending interlude first.
Values Dissonance - At one point, it is revealed that Rider feels insecure about being too tall for a girl. This is an issue that a lot of real life girls can relate to... Except for the fact that Rider is only 172cm tall, which depending on where you live, could be considered as rather short. More than value differences, it shows the differences in height standards between different societies.
The Woobie - Practically every character in the game is this, to some extent. Even the Complete Monsters would have a case, were they not Complete Monsters... However, Sakura stands out as the worst case, by some distance in the original game.
The Scrappy - Some fans see Sakura as this due to her villainous actions in Heaven's feel combined with various reasons, such as her route being rushed and being right after Unlimited Blade Works with its high popular heroine, Rin. Others see her as The Woobie even to the extent she's treated in most side materials.