Innocent Blue Eyes

Innocent "baby blues" or clear, pure, and shining, these eyes are blue to symbolize youth, naivete, inexperience, and purity of soul. Either way, a popular choice for heroes and heroines and younger characters. In older works, Gray Eyes was used for this instead. Common with Hair of Gold. Contrast Icy Blue Eyes.

No real life examples, please; Even if eye color had a meaning in Real Life, so many people have blue eyes that we'd be here all day.

Examples of Innocent Blue Eyes include:

Anime and Manga

Belldandy of Oh My Goddess! fits the first variation of Blue Eyes quite well—complete with Hair of Gold (usually).
Guardian of the Sacred Spirit has Prince Chagum, who carries the egg of a benevolent water spirit. He also has a noble, innocent personality typical of blue eyes.
Sailor Moon/Usagi herself has big innocent blue eyes and several people comment on how beautiful they are.
Slayers: the eternally optimistic Amelia and the kind and polite Sylphiel both have blue eyes of this kind.
The OVA and TV series of You're Under Arrest gave Miyuki Kobayakawa the clear blue variety.
Quatre Winner from Gundam Wing has the 'innocent' type, as well as Duo Maxwell.
In Neon Genesis Evangelion, Shinji's deep blue eyes fall into the "pure" or "innocent" category (at least, when he first started out) and were chosen for that exact reason — although the Manga depicts him with brown eyes.
Fullmetal Alchemist's Winry has very bright blue eyes, which she got from her parents. Her eyes probably fit the first meaning.
Mikado from Durarara!! is a subverted bait-and-switch of Innocent Blue Eyes. Early in the series, the audience thinks he's your average Naive Newcomer, trusting and uncorrupted by Ikebukuro city, but later, we find out he's actually been the cold and calculating chessmaster and leader of the dollars this whole time, has been Obfuscating Stupidity, and is the type of person you don't want to cross. On one occasion, he actually shivved a guy with a pen. It's at this point that you realize they were actually Icy Blue Eyes all along.
Reinforce Zwei of Magical Girl Lyrical Nanoha has the bluest eyes of the series, emphasizing the childlike innocence of the character, as well as her magical nature (The first Unison Device created since the days of Ancient Belka) and her affinity to ice.
Kimba the White Lion has the innocent/deep-blue varient.
Yuuen of Wild Rock has absolutely huge blue irises of the innocent sort and Hair of Gold to match.
There are several blue-eyed characters in Baccano!! that are harmless and (relatively) innocent (Eve, Isaac, Carol, Mary).
Chrono Crusade has a couple of different examples. Siblings Rosette and Joshua Christopher both have blue eyes with Hair of Gold—as children, they both seemed to have it to represent innocence, but as they get older, Rosette becomes The Hero, while Joshua goes insane after being recruited by the villains, and then they're definitely the "icy" version. Joshua's eye color could also represent his lost innocence.
Vash from Trigun has softer, kinder innocent turquoise eyes in contrast to his twin brother's lighter, icier gaze. This difference may represent their different personalities.
The eponymous Naruto has more of the innocent type of blue eyes, though he does have a mischevious streak.
Tenshi ni Narumon: Noelle's big baby-blue eyes totally fit into the "pure and innocent" category, together with Hair of Gold. Besides, she is a heroine.
The Thompson sisters in Soul Eater have blue eyes and blonde hair, but neither are innocent. Probably used to indicate they're American.
Amati from Spice and Wolf has the "baby blues" variant, emphasizing his youth. He even has Hair of Gold.
Negima:
- Nodoka, the resident Shrinking Violet, has blue eyes in the first anime series and the Ala alba OAD series. (She gets purple eyes in the manga and red eyes in Negima Second Season.) Rarely visible in the anime series, but as she came out of her shell between it and the OAD series, you see them a lot more there.
- The Innocent Robot Girl Chachamaru gets Blue eyes in the first anime series (she gets green eyes in all other adaptations).
As a superhero with the personality of a wide-eyed Ingenue, it's only natural that Keith Goodman from Tiger and Bunny has Innocent Blue Eyes.
Alfred F Jones, the personification of the USA in Axis Powers Hetalia, has light blue eyes due to Phenotype Stereotype. His role as a Love Freak with Chronic Hero Syndrome put him here, but it's played with since he's also a bit of an Attention Whore and his naiivety borders on just being plain clueless sometimes.
- However, as a child, he is a straight example of the trope.
Hinako from Bitter Virgin is a tragic example, considering her status as a Broken Bird.

Comic Books

Captain America (comics) has blue eyes, along with Hair of Gold.

Film

In 28 Days Later, Jim's wide-open baby blues leave him looking innocent and rather bewildered (right up until the...rescue scene).
Michelangelo's eyes in the 2007 CGI Teenage Mutant Ninja Turtles movie are blue, while the other Turtles have brown eyes. This gives Mikey a more innocent look, befitting his personality.
Atonement's Robbie Turner has an impressive pair of big blue eyes. It's coherent with the director's interpretation of him as a character Too Good for This Sinful Earth.

Literature

Jake has blue eyes which, at the beginning of The Dark Tower series, fit into the innocent category, but as the story goes on, they're described as being eerily similar to Roland's icy eyes.
In the second book in the Darkest Powers trilogy, Tori mocks Chloe for having blue eyes and Hair of Gold, saying she is “just like [her] sister” - essentially useless and always in need of saving. Chloe, though angry about Tori’s insults, has to admit that this is kind of true, since Derek has to come running to her rescue quite a few times in all three books. Liam also comments on her eyes, saying they make her look cute and scared and thus very desirable, much to the anger of Derek.
In John C. Wright's Fugitives of Chaos, Mortimer has innocent blue eyes as well as the mind of a 5-year old.
Luke and Ben Skywalker both have blue eyes that can swing from innocent to icy at fancy's whim, and often quite suddenly, to the point where it scares Ben (to a small extent, anyway).
Rand Al'Thor in The Wheel of Time is first described to have wide, innocent blue eyes. As the books progress, they change into the piercing, ice cold type. They switch between gray and blue as well.
The Three Musketeers: The musketeer Athos has "azure" eyes, presumably as a symbol of his pureness.
In Darkness Visible, William and Amelia Marsh have blue-green eyes. In Amelia's case, they show innocence. William starts out as innocent, but is definitely veering towards piercing and cynical by the end of the book.
In A Song of Ice and Fire, Sansa's eyes are said to be particularly vibrant and lovely, arguably an indication of her innocence and goodness (at least to start with).
- Brienne of Tarth is a very large, very strong, very ugly woman. Her one beauty is her innocent, sky-blue eyes.
A couple of these in the Deryni works:
- Sean Lord Derry, Morgan's aide-de-camp, is human, but Morgan introduces him to the use of magic as part of his reconnaissance missions. When Morgan teaches him Mind Speech, Derry's "blue eyes were wide, but trusting."
- When confronted by a guardsman in Deryni Rising, Duncan McLain staged dropping his tabernacle key and "turned innocent blue eyes on the man". Duncan is also a Deryni (and as such, forbidden to be a priest), so cultivating this innocent look is important to his protective arsenal.
Derek Huntsman in Domina.
The mother in L. M. Montgomery's Jane of Lantern Hill. This is explicitly contrasted with her own mother's Icy Blue Eyes.
Bertie Wooster, Spoiled Sweet Upper Class Twit of Jeeves and Wooster fame.
Peeta Mellark, the Nice Guy of The Hunger Games.
Shannon and Ginevra in Doctrine of Labyrinths are both extremely sheltered and naive and have wide blue eyes.

Live-Action TV

Sheldon Cooper of The Big Bang Theory has large, expressive, very innocent sky blue eyes. They may or may not be a physical manifestation of how clueless he is when it comes to social interaction, despite his intellectual brilliance.
Archie Kennedy of the Horatio Hornblower mini-series has the "innocent and sweet" variety.
Chris Colfer of Glee is sometimes blue-eyed, sometimes green, sometimes gray, depending on the lighting. Just look at his eyes when he's with his father in any scene, they're likely to be of the wide and innocent type. Judging by his intentional lash-fluttering when Finn tells Puck to stop pushing Kurt into lockers, the character appears to be aware of this trope.
DG inTin Man has big blue eyes of the "innocent" type.
Stargate SG-1‍'‍s Samantha Carter has a vibrant pair of baby blues. They fit her personality quite well.
Invoked in Star Trek: The Original Series episode "A Piece of the Action." Regardless of the fact that it wasn't applicable.

Gangster: (pointing a tommy gun at the landing party) And don't give me those baby blue eyes.
Dr. McCoy: (who is very blue-eyed and very dangerous) *more startled than before*

Video Games

Thrall from Warcraft has blue eyes that are actually both "baby blue" and piercing. That is, the colour looks both innocent and quite striking on an orc. Given his personality, that is probably exactly the intended effect. It also stands out, considering many orcs have red eyes as a result of the demon blood they drank (Thrall's parents didn't).
Liara T'Soni from Mass Effect has bright, innocent blue eyes, matching both her personality and her skin color.
- Liara's eyes make for an interesting commentary on her alignment throughout the series. In the first game, she had the innocent blue variety, in stark contrast to her mother's darker, more piercing shade. In the second game, Liara's eyes become a darker but no less vibrant shade of blue, reflecting her hardening nature as she becomes more ruthless and vicious while hunting the Shadow Broker. It is most noticeable in the Lair of the Shadow Broker DLC, where her face is visible without being lit by multiple orange holographic displays. However, if you carried a relationship over from the first game and re-established that relationship after the mission, she's back to the same baby blue she had before - perhaps reflecting your influencing her back to her old, optimistic worldview.
In Lightning Legend Daigo no Daibouken, Cheerful Child Yuki Shirogane has this type of blue eyes. It's even pointed out in her in-game character profile, as the "distinctive features" part of it mentions: "Long hair; Big round eyes".
Slippy, Fay, and Tricky from the Star FOX series.
Flynn Scifo has Innocent Blue Eyes to match his Hair of Gold. He is, appropriately, a Knight in Shining Armor.
Tails from the Sonic the Hedgehog series, though his eyes are a bit darker than is usual, he is no less innocent.
- Maria Robotnik also counts. She is an innocent pacifist, and she also has blond hair.
Sora, Roxas, Xion, and Ventus from the Kingdom Hearts series. Although Xion is also depicted with Kairi's purple-ish blue eyes on some artworks.
Kirby, of course.
Red, the Idiot Hero of Solatorobo. Director Frasier from the orphanage in Basset comments how Red's eyes tell her he's a good person.
Pac-Man has been given a dark blue, almost purple-ish blue, variation in recent installments.

Western Animation

Timmy Turner of the Fairly Oddparents. His Blue Eyes represent his youth, he's ten years old, and arguably his innocence. He is also arguably the hero of the series, albeit a Designated Hero many times.
SpongeBob SquarePants himself. He has an innocence about him. He is, also, the hero of the series, or at least, he is so in the movie.
While Recess uses a standard Black Eyes style, Word of God says that T.J. has blue eyes. He's nine years old and very youthful, has an innocence about him, and is also The Hero of the show.
Charlotte from Making Fiends is an odd example; every human character is completely one color, and she is baby blue. This trope could be why, rather than using pink or yellow or something more "fitting" for her personality. She fits the character type, being innocent, childish, naive, and optimistic. It causes her to contrast with Vendetta, who is completely moss-green, filling in for the negative Green Eyes.