Poor Zack Martin from Suite Life... He once did a load of laundry with candy in his pocket and it turned his underwear multi color. Which is lampshaded when Maya notices.
Maya: It takes a man to wear rainbow underpants.
Zack: They were white til' I did a load of laundry with candy in my pocket.
On an episode of The Big Bang Theory Howard talks the gang into going to a bar to pick up women. They all change out of their standard Superhero symbol boxers ... just in case.
On Chuck, super tough NSA agent Casey got caught wearing ones with lucky red clovers all over them [he's handcuffed to a headboard at the time]. "It's like Prague again, eh Casey?" In one of the Chuck comics, he has a Hawaiian print pair!
On Cougar Town, financial manager Andy Torres, who is about to meet with an important potential client, demonstrates that he is wearing his "lucky" boxer shorts by pulling them up to show the "wiener dogs and balloons" pattern.
In the Monty Python sketch "How to identify different parts of the body", a recurring theme is the identification of "Naughty Bits" — shown as white boxers with red polka-dots. Recurrences include "the naughty bits of a horse" — a horse wearing similar boxers, "the naughty bits of a lady" — a woman wearing boxers and a particularly modest bra in the same pattern, and "the naughty bits of a cabinet minister" — picture of a cabinet minister with polka dot boxers superimposed on top of his clothes
A hilarious moment in the popular season 1 episode of Veronica Mars, "An Echolls Family Christmas", features several poker players stripped down to their boxers. Duncan and Logan were wearing identical ones (blue with reindeer heads).
In his 60th anniversary special, Mickey Mouse was stripped to a pair of boxers with orange polka dots by an angry wizard. (Mickey had "borrowed" some of this wizard's magic to impress the crowd gathered at the celebration).
iCarly: Spencer with his duck pajamas. Then his duck boxer shorts. Sam and her "I love Las Vegas" underwear. Freddie's anti-bacterial underwear would be related to this trope somehow.
Survivorman had Scooby-Doo boxers, but it's unclear if he owns some, or it's just part of the "props of items average joes would most likely have if lost".
Tim's union jack boxers make several appearances in The Goodies, most notably in "The End" and "Scoutrageous".
And in Saturday Night Grease he dons a pair of underpants that have a large carrot on them.
Booth had Christmas boxers in "The Man In The Fallout Shelter" on Bones.
This was a Running Gag on BeetleBorgs. (Visual gags where someone's pants fell down - combined with goofy underwear - happened all the time on the show. For example, Count Fangula had ones with bats printed on them.)
Other men's underwear
One episode of Man vs. Wild revealed that Bear Grylls owns a pair of Union Jack briefs. (This may have been a set-up, though.)
In Dead Like Me, Mason is shown multiple times wearing nothing but his Union Jack briefs. Which was enough for George to demand he moves out of her apartment.
Childish women's underwear
On The Daily Show, Kristen Schaal promised to take off a piece of clothing for every sexist comment made by the news media. At first she tried to stop after just taking off her earrings and coat, but Jon Stewart pointed out they had a lot more clips, and she ended up standing in nothing but her Wonder Woman underoos.
On My Wife and Kids, when Michael and Junior were renovating the garage with Franklin, Franklin stoops down, revealing the pink panties Kady (his girlfriend) gave him. Michael and Junior go on to admit that they got the same gift from their significant others.
Not underwear per se since its part of a full body suit but Akibablue has a teddy bear print across her buttocks underneath her outfit's skirt which is clearly meant to evoke this trope.
Daisy Wick owns multiple pairs of "day of the week" panties in Bones. She first shows off her "Monday" pair in the first episode of the sixth season (to distract a bunch of men who were threatening her and Brennan), and the "Tuesday" pair was seen draped over the couch a few episodes later, when Booth and Brennan walked in on Wick and Sweets mid-coitus.
Nelson Muntz is forced to wear his mother's frilly pink panties in one episode of The Simpsons. (The Muntzes are so poor that they have only one pair of underpants between them.)