Played with in Fate/hollow ataraxia when the cast gets drunk and then adds animal tics to their speech such as nya! (cat) or wan (dog) based on what their favorite animal is.
In Fate/stay night itself, Saber has a particular way of pronouncing Shirou's name (she stresses the wrong syllable) that is subtle enough that many English speakers don't pick up on it, but in-story is said to be very distinctive. Rider makes a similar mispronunciation.
Moran in Shikkoku no Sharnoth often answers statements or questions with either 'Yes. No.' or 'No. Yes.' followed by an explanation.
Misuzu Kamio in AIR, who is fascinated with dinosaurs, often says "Gao" (her idea of the sound a dinosaur makes) when surprised, distressed or embarrassed.
Gao is the sound a dinosaur makes in Japanese. (For extra credit, look up the Japanese word for a dog's barking.)
Kanon is full of such characters: Nayuki ("nyuu"), Makoto ("auu"), and Ayu ("uguu"), to the point of being overdone. It adds tremendously to the moe factor of the girls though, especially in Ayu's case - it's just so darn cute, which it is also helped by the marvelous performance of Yui Horie, Ayu's voice actress.
Though not a heroine, Sayuri Kurata from Kanon tends to say "ho-e?" in addition to her more usual "ahaha." Whether or not this is influenced by Sakura from Cardcaptor Sakura is unclear; although, due to Sakura's Genki Girl personality, her ho-es are usually much more verbal.
Nagisa Furukawa is fond of ending her sentences with desu~.
Also used for a Deconstruction which is then Played for Laughs: Tomoya suggests that Sunohara says 'and a toilet seat cover' at the end of every sentences. Sunohara did so, but in the end, frustratedly complain that it's ruining every serious sentences that he'd say.
Kotomi Ichinose has a habit of ending her sentences with "-no".
Little Busters! has 'wafu~' for Kud, which she uses all the time, and 'fuee' for Komari, mostly as an expression of surprise.
Rena Ryuuguu has a habit of repeating the final words of sentences, most famously kana, kana (I wonder, I wonder). More to the point, "kana kana" is supposed to be the sound higurashi cicada make. She also has her "Hau!" exclamation whenever she goes into "I'm Taking Her Home with Me!-mode". At one point Keiichi directly tells her "Stop 'hau'-ing, already!"
Satoko Hojo has a habit of speaking with over-formal grammar and ending her sentences with wa, giving the impression she's trying very very hard to sound like The Ojou. Her actual reason is her family was hated by the villagers so she tries to sound ultra-polite so that others won't hate her. Satoko also uses "nii nii" to refer to her older brother, which sounds childish, but is also the name of a different kind of cicada.
Rika Furude likes to use nipaa~ (an onomatopoeia for 'smiling') and mii (a kitten meowing, translated in the English release of the manga as "mew"). Technically, not onomatopoeia but phenomime. Rika also has a habit of saying "nano desu" after her sentences, which is translated as "Sir" in the official manga translation (she uses sir for everyone, including her friends, no matter their gender).
Hanyuu's trademark is a cry of au au au! when she is upset.
In the second episode of Higurashi Kira, Fairy Hanyuu ends most of her sentences by saying her own name.
Maria has her trademark "Uu~." This actually has some significance to the plot. One day she forgot the words to a song, so she replaced the words with an "uu-" sound. It made her mother smile, so from that point on Maria believed that saying "uu-" was a spell for happiness. It's also something of a deconstruction; if her mother is to be believed, the weird speech pattern is one of the reasons why she's bullied in school and has no friends. It's certainly the reason said mother smacks her because she finds it irritating.
In the English translation of the visual novels, Dlanor A. Knox always puts emphasis on the last word of every SENTENCE. Which is written in UPPERCASE. The Japanese version has her end her sentences in copulas written in katakana.
"Reporter Spark Brushel Has Obvious Verbal Tic, Often Speaks in Newspaper Headlines!", end quote.
Det. Gumshoe ends most of his sentences with "pal" when he's addressing someone, pal. In the Japanese version he slurs the end of his sentences. He doesn't like it when someone tries to copy his verbal tic:
Mu, in the Japanese version, Miles Edgeworth would appear to start his sentences with a thoughtful little noise.note "Mu" roughly equates to "hm" in English.
Zvarri! Luke Atmey has seen that you've forgotten him!
Florent L'Belle absolutely LOVES to PEPPER his speech with ALL-CAPITAL LETTERS, likely to simulate him EMPHASIZING those words when SPEAKING. It's yet ANOTHER way to tell that he is OBVIOUSLY one of The BEAUTIFUL Elite, and therefore FAR superior to all of YOU unwashed peasants.
Ah ha ha ha ha ha! He also tends to laugh at the beginning of sentences when he is mocking someone or passing something off as being incorrect.
Now, now, now. Especially near the end of Case I-3, Ernest Amano likes to begin sentences in a way seemingly to break up fusses/arguments.
Blaise Debeste has a verbal tic, y'know, and if you can't tell what it is then you're an even bigger idiot than his son, y'see.
In Brass Restoration, Minori has a habbit of saying "Nyu, Nyu" when Ryo teases her or she's stressed. Kouri also says "Pigyuu" occasionally.
In Katawa Shoujo, Misha loves to add "Wahaha~" to the ends of her sentences. And her beginnings. For that matter, she'll just randomly say it.
Yasuhiro Hagakure ends a few of his sentences with "-be". This has been translated by the thread as "'right" (which is as close to the connotations of "be" in a Tohoku dialect that one can get with a single English word). Monobear/Monokuma's "upupupu" could possibly also count as one, to a lesser extent.
In the official English localization, Hagakure's tic is translated as "for serious".
Chiaki Nanami tends to end her sentences with "...I think". The one time she expresses certainty about something the other characters note how out-of-character it is.
In Virtue's Last Reward, Sigma has a rather unusual tic of "talking like a cat whenever talking about cats". This results in a good number of cat puns, and a number of interesting reactions from the other characters.
Sigma: Oh that? It's a book meow-ht cats.
Alice: A...meow-ht, cats?
Sigma: Oh, sorry. It's a sorta...tic I've had since I was a kid. Can't help talking like a cat when talking meow-ht cats.
On the same page, "Zero Jr.", an A.I rabbit, has a tic that he speaks in rabbit puns.
Zero Jr: All you need to know is that anybunny who tries to sneak out gets hit with a biiiig penalty.