Subverted with Germany where he's shown wearing blue boxers with a patch sewn by Austria.
In a filler episode of Dragon Ball Z, a girl caught Gohan wearing teddy bear print boxers, and threatened to tell the school about "his secret" unless he went on a date with her (and she actually thought the boxers only added to his cuteness). However, Gohan thought she'd caught him removing his Great Saiyaman costume.
Averted in Fullmetal Alchemist — Edward's boxers are plain and boring. However in a bonus-comic Arakawa is shown asking her assistants to try to design his underwear, and got some interesting suggestion such as Automail-boxers.
In Is This a Zombie?, Orito ends up in purple flower-print boxers during one of the OVA episodes.
Katekyo Hitman Reborn!, The entire beginning of the series, especially when it comes to our favorite little Dying Will Bullet that burns off all your clothes (except your underwear, in most cases). As a matter of fact, Tsuna seemingly has a different one each and every time. The boxers return again when Spanner captures him... well... you know the rest...
In Episode 2 of the Little Lulu anime, when Tubby strips down to his underwear as one of his tactics to try and scare Lulu, he is shown to be wearing a pair of navy blue boxers with sky blue splotch patterns on them.
Ranma is often seen wearing underwear with his name (or the first syllable thereof) printed all over it.
Also when Tsubasa is revealed to be a boy despite dressing and acting like a girl he is shown to wear pink boxers with yellow smiley faces on them.
Several characters in the Pokémon anime are shown wearing white/blue striped underwear, including Ash, a Hitmonlee's trainer in "The Punchy Pokemon", and Meowth imagines Giovanni wearing them while trying to cool down.
Classy Cat-Burglar Carson D. Carson spends most of Project Eden (The Dirty Pair movie) running around in his pink with green polka-dot boxers after the girls confiscate his clothes.
Soul Eater's eponymous Soul apparently wears blue boxers with bones on them both in the manga and the anime (and since the series was animated by BONES...yeah).
The eponymous Space Dandy is revealed to wear black boxer briefs with lightning bolts on them; as first shown in the episode "The War of the Vests and Undies."
In one episode of Yu-Gi-Oh! GX Jaden is shown in boxers with his teacher's cat printed all over them.
Other men's underwear
In one of the K manga, Reisi Munakata, the Blue King, takes his jigsaw puzzle hobby far enough to have a jigsaw-puzzle print on his underwear. Briefs, not boxers, of course, for fanservice.
In the Cloverway English dub of Sailor Moon, a little boy drops his pants in front of Rini and says "I wear Sailor Moon underwear!" though he is shown holding plain looking briefs in one hand and his shorts in the other. In the original Japanese, he tells Chibiusa "Look at my little elephant!", doing his impression of Crayon Shin-chan.
In a similar, offscreen example, Tsukasa in Lucky Star is particularly embarrassed by absent-mindedly wearing character print underwear on Measuring Day.
Also similarly, Yuno in Hidamari Sketch was also hugely embarrassed when her kitten-print undies were revealed in a locker-room prank. (Why does it have to be yonkoma...?)
On the cover of Bleach volume 3, you can see that Orihime's wearing polka-dot underwear.
A Running Gag on Blue Seed involves Momiji displaying a different animal on the seat of her underwear when she does her Once an EpisodePanty Shot. The other characters maintain a betting pool on just what's going to show up on her panties any given day.
Parodied by (what else?) Bobobo-bo Bo-bobo, in which Don Patch wears panties with ribbons on them, and he makes no effort to hide this (yes, he).
In a Running Gag for Detective School Q anime, Kyu (but not the viewer) ends up seeing up Megumi's skirt for a variety of reasons (though never because he intentionally flips her skirt up; sometimes the wind blows strongly while she's wearing a short skirt, at others she trips on her feet...) and blurts out what pattern is on them on a semi-regular basis. The patterns include things like teardrops and bunnies.
In one of the episodes of the second season of Sayonara, Zetsubou-Sensei, Ikkyu is so distracted by Chiri's Bell Pepper panties that he manages to forget that they were attacked by an alien race piloting Humongous Mecha.
Kuro of Today's Cerberus is said to have bear panties in chapter 2. We don't see them then, but we do see them in a side-chapter which features Kuro actually purchasing the underpants.
The movie Ultimate Teacher has Ganbachi humiliate Hinako by removing her skirt in front of the whole class... revealing her lucky kitty gym shorts. Naturally, men from all over rush in to have a look. Hinako's maturity is later reflected when she defeats a gang by showing that she's now wearing plain, white panties.
Penny in Zatch Bell! has underwear with her one-sided boyfriend (Zatch) on them. Then, she accidentally reveals them to Kiyo's class. Their reactions are epic.