Manfred von Karma, named after the Red Baron. They were both brought down by a single bullet. You could say that karma came back to bite him in the ass, fifteen years later. "Manfred" also means "one who brings peace," which is appropriate for a prosecuting attorney and, in a twisted way, for a murderer as well.
There is the original eponymous character. Phoenix Wright, who rises from the ashes and flies. Comes back from the dead. Has turnabout trials, and is nearly defeated seventy-three times every trial. His Japanese surname, Naruhodo, is a play on a phrase that means "Yes, I see."
Miles (Irish, meaning "warrior") Edgeworth and Reiji Mitsurugi ("honorable blade") are both references to the character's rapier wit and confrontational, sharp nature. "Honorable blade" is also a hint at his Character Development.
Then there's the downright diabolical ones that can even give you a few hints as to the character's true nature. Calisto Yew—Calisto is a butterfly, yew is a kind of poisonous plant, referring to the butterfly/flower symbols of Cohdopia.
And there's also those which leave nothing to imagine, like Quercus Alba's name in the Japanese version, Carnage Onred.
Byrne Faraday. Byrne? Gaelic for raven.
Trying to count the meanings in "Dahlia Hawthorne's" name would surely take a while, but the most important ones are the murder mystery The Black Dahlia, the Hawthorne Effect (of which she's a perfect example) and the fact that her name spoken out loud sounds like "The liar has thorns". To make it even more perfect, her sister's name, Iris, is, in fact, a direct translation from her Japanese name, so the whole flower-thing was partly a coincidence, which just happened to fit.
Also, the entire Fey family, a family of spirit mediums. The word fey means "Having or displaying an otherworldly, magical, or fairylike aspect or quality."
Matt Engarde's name seems a little off- he's a very easy-going person- until you realize that he's actually the Big Bad of his game and the gentle personality was an act.
Furio Tigre, the tiger to Phoenix/Ryuuichi's dragon.
This also stretches beyond characters as well. Case three of Apollo Justice: Ace Attorney features a fictional made up disease named "Incuritis" that is incurable. Well, save for an extremely hard to get drug that can only be brought into the country illegally.
And then in Investigations 2, you have two chemicals. Normallium is in normal every day things such as paints and washing detergants and is not deadly at all on it's own. And the other, Fatallium, is only found in very select things such as powerful and fatal pesticides that aren't sold to the general public. Combining the two, results in a chemical reason that forms a deadly poisonous gas.
The main character, Emiya Shirou. The first kanji in the name Emiya means "protection". Shirou is spelled with the kanji for "soldier" and "son". As a word, "shirou" means "white", and can carry connotations similar to the English phrase "white hat". All of these fit with Shirou's character and backstory.
Rin, the Tsundere, writes her name with the kanji for "cold". The word actually means an "official", fitting with Rin's role as administrator of the land used for the Grail War.
Sakura's name means "cherry blossom", which is significant for reasons explained on that page.
Having a name that means "beautiful" is a sick joke that life has played on Kotomine Kirei. It is also an appropriate reference to the prayer "Kýrie Eléison", meaning "Lord, have mercy!" (which, later in the story, is the prayer Kirei uses to exorcise Zouken).
Kirei's backstory reveals that his name actually invokes this trope; his father gave him this name specifically because of those two meanings, hoping they will affect who his son grows up to be. A sick joke, indeed.
Fujimura Taiga has much in common with tigers. She even wears a yellow and black striped shirt. She seems to acknowledge this (she's named her kendo stick Torashinai, "tora" being Japanese for tiger), but whatever you do, don't call her Tiger.
Mion in Higurashi: When They Cry. Both their names are written with the kanji for "oni," as is the tradition in the Sonozaki family. In keeping with this, Mion has an oni tattoo on her back; in general, oni are very significant throughout the question arcs of the series.
There's a certain amount of Theme Naming going on with the witches; Beatrice, Virgilia and Clair Vauxof Bernard are named for characters in Dante's Divine Comedy. Maria, the Witch of Origins has the power to create a soul out of the void.
The Seven Sisters of Purgatory. All named various names of The Devil, the most obvious being Satan and Lucifer. Rather brilliantly, their "sins" are all related to that particular name, such as Lucifer being Pride: in the Bible, The Devil was known as Lucifer as an Angel who fell from Heaven because of pride. Mammon is used to refer to greed, etc.
Despite Battler's name not being a plausible one in real life, it relates quite well to his personality; the kanji in his name literally mean "fighting person".
Hisao is written as "long time [of absence]" (久) + "man/husband" (夫), the former being a reference to his months-long hospitalization, and the latter meaning of the latter being what he could become to the girls.
Emi means "Smiling Beauty", which fits her cheerful, energetic personality which turns out to be a more of a facade.