Prince Zuko's have been treated with the least subtlety since the Agni Kai sequence in the third episode that had the fangirl favorite stripped to the waist and fighting a duel to the death with Zhao, complete with impressive flexing, posing, and dramatic sweating. A shot in the Beach Episode actually included a huge flock of white birds passing behind him as he throws away his shirt, complete with blushing fangirls and floating hearts.
Sokka gets a few, including one when helping to forge a sword, which means plenty of sweat.
Batman Beyond has to have special mention for not only more than a few shirtless Terry moments but a lovely five-second scene of him in the shower after escaping Stalker. There's some fanservice one can agree with.
In the episode "Out of the Past", a younger (or less old?) Bruce Wayne half-naked for the entire episode after getting out of the Lazarus Pit.
The Backyardigans: During the episode "Legend of the Volcano Sisters", the three boys are all shirtless to match the ancient Hawaiian setting. Also, during "Heart of the Jungle", practically 10% of Tyrone's chest is covered when he is wearing his Tarzan costume.
On Code Lyoko, the boys get a few such scenes, especially Ulrich. Most notable is the Getting Hot in Here moment in "New Order", or the opening of "Bad Connection" where Ulrich is wearing just a Modesty Towel in the hallway (Aelita and Yumi at least pretend to be looking away).
On Xiaolin Showdown, Raimundo is shirtless in exactly three scenes, but there are still dozens of forums dedicated to those few seconds with some very creepy comments on the pictures.
In Bravestarr, according to commentary for the pilot movie, they specifically had a scene of Bravestarr shirtless for the ladies in the animation department. Filmation would have probably have done this a lot more, if so many of their heroes weren't already Walking Shirtless Scenes.
Done for comedy rather than fanservice in Adventures of Sonic the Hedgehog, where Robotnik gets far and away the most Shirtless Scenes. He's been depicted nude a few times, too, and he was in a bikini for a brief instance in "Hero of the Year", to highlight his narcissism.
In "Sonic Gets Thrashed", "Zoobotnik" (although in that case he was at least in a bath), and a couple of others.
Done for comedy andfanservice in every episode of The Fairly Oddparents that features Juandissimo, who tears his shirt off with only his bulging pectoral muscles, then eventually regenerates it with magic, seemingly for the sole purpose of doing it again.
Family Guy: News anchor Tom Tucker in Meg's fantasy in "The Kiss Seen 'Round The World" (also a spoof of the infamous "pool scene" in Fast Times At Ridgemont High).
The fight between Shane and Killbane in Galaxy Rangers episode "Mindnet."
Jonny Quest TOS. Jonny and Race got to be shirtless quite a lot during the series. Dr. Quest and Hadji also doffed their tops a few times.
Codename: Kids Next Door: Numbuh 4, or Wally Beetles, despite being 10 years old, has quite a few moments where he's seen shirtless. Though those moments had enough poularity that quite a few fan artists like to draw him shirtless very often, and even sometimes poking fun at those moments.
Recess: T.J. Detweiler (despite being nine years old) was given a shirtless scene in "The Big Prank", when he has to be King Bob's "fanner boy", leaving him walking around in nothing but his boxers and hat. Considering that he's underage and pretty chubby, it can be considered Fan Disservice.
Redakai: Ky Stax is given this in "Neptune's Reef". Twice, in a swimsuit, played for Fanservice.
Boomer also got this once in the same episode
In the "This Year's Model" episode of Daria, during the open modeling class, Claude from the Amazon Modeling Agency has the boys take their shirts off and then instructs the girls to rub the boys' naked chests.
Total Drama's guys tend to get shirtless. Among the most notable: Justin, Alejandro, Trent, Duncan, Cody, Noah (in his swimsuit) and Geoff.
Lance has several of these in Sym-Bionic Titan. It's fanservice, although to be fair, it's usually in the privacy of his own room.
Dipper gets one in Gravity Falls, in the episode "Dipper vs. Manliness".
Brock Sampson consistently in The Venture Bros.. In "Victor. Echo. November" he even gets completely nude and covered in blood, and in another episode he has a dream where he rides a dolphin naked.
Most of the male main characters in Young Justice have been shirtless, much to the delight of fangirls.
Aqualad was shirtless in the following episodes: "Infiltrator", "Welcome to Happy Harbor", "The Fix" & "Complications"
Blue Beetle was shirtless in "Beneath", "Before the Dawn", "Runaways" & "Cornered"
Kid Flash was shirtless in "Infiltrator"
Match (Superboy's clone) was shirtless in "Agendas" & "Auld Acquaintance".
Speedy/Red Arrow/Arsenal was shirtless in "Auld Acquaintance".
Superboy was shirtless in "Infiltrator", "Denial", "Bereft" & "Targets".
Red Arrow & Superboy also wore bare-chested circus clothes in "Performance".