There's an ad for Five Hour Energy, where a guy gets up, grumbling about how he hates mornings, until he pulls out the product, then the next we see him, he's dressed and shaved, saying "Let's do this!" If you watch the commercial beginning to end, you may notice he looks about 10 years older when cleaned up.
An advertisement for Zzzquil, a sleep aid, depicts a number of people looking goofy while sleeping, then at the end shows an attractive woman waking up smiling with messy hair and bright, sparkling eyes. The point seems to be that you'll sleep deeply (the goofy sleeping people) and wake up refreshed (the attractive woman waking up).
Anime and Manga
Cher from Wolf's Rain usually has disheveled hair because of her hectic working conditions.
There's also France, who's hair England envied when he was young but was described by Canada as unkempt.
L from Death Note looks like he just crawled out from under the bed with hair that he probably never brushes, solid black eyes, extreme bags under said eyes, wears the same plain, baggy clothing every single day, is extremely pale/thin, and Does Not Like Shoes. That doesn't stop him from being Mr. Fanservice.
For that matter, whenever Asuka gets rid of those ridiculous signature hair clips of hers, but especially near the end, when she just stops caring, manages to look infinitely more mature.
Yuki from Wandering Son used to wear a lot of makeup and wore a wig whenever she was outside; she honestly looked more like a drag-queen then a woman. In recent volumes she's ditched the makeup and grown her hair out. Her hair is apparently not all that combed either, and she's switches between casual and feminine attire often.
Takatsuki's hair is often unkempt, though she does also tend to comb it into a very tidy look.
Ouran High School Host Club: As shown in episode 17, Kyouya still looks good even when he's literally dragged out of bed in frumpy clothes and bed hair.
And Haruhi Potter looks adorably frumpy. In fact, Haruhi often looks her most adorable in clothes that don't look like they cost a small fortune.
Souta's novelist sister Izumi from WORKING!! doesn't wear makeup, constantly has ink smudges on her face, has moderately messy hair, and just has a bedraggled appearance in general. Still, she is no less beautiful because of this, but is possibly more beautiful because of it.
The women in Attack on Titan, as a result of being soldiers. They don't have time for (or presumably access to) cosmetics, and most simply wear their hair short or put it up in a messy ponytail to keep it out of the way. This doesn't stop them from being attractive, in particular Krista.
Casca from Berserk is often noted as one. Being a mercenary, she keeps her hair short and wears men's clothing and non-Stripperiffic armor. While people do comment on the way she dresses, she is often considered to be very beautiful.
Withnail and I. Both title characters wear odd clothing and look like they haven't combed their hair in days, yet are nonetheless fashionably unkempt.
In Better Off Dead, French foreign-exchange student Monique looks very sexy fixing Lane's car with grease on her face.
In the old John Wayne and Robert Mitchum western El Dorado, Mississippi ends up in a brief scuffle with the daughter of a nearby rancher when he thinks she is one of the bad guy's Mooks sneaking up on the Sheriff's office. Mississippi remarks after they stop fighting that she looks like "A mustang in need of a comb".
In the Fearless books, Gaia Moore is often described as beautiful, despite the fact that she usually just wears whatever clean thing she can pull out from under her bed.
In one book, a male character rates females on the "Firehose Scale," which measures how attractive a girl would be immediately after being blasted by a firehose.
In the Symphony of Ages Rhapsody gains an unearthly beauty after traveling through the pure flame at the center of the world. Virtually every man she encounters after that are dumbstruck by her beauty, even though she's usually wearing highly practical clothing. Even when she was clad in rags, mud, and various pieces of debris from bushes, her beauty was enough that many locals mistook her for a nature spirit.
Piper from The Heroes of Olympus is described as looking beautiful to Jason, even though her hair is cut choppily, she's wearing a jeans and a parka, and her t-shirt is all torn up.
Eponine from Les Misérables. We're told that a life of poverty has been horrible to her, and now she's skin and bones with stringy hair, probably smudges of dirt, an unhealthy mind, even missing teeth. Despite all of this, she still looks good enough to be described with a star metaphor at one point.
In Zilpha Keatley Snyder's The Changeling, Ivy Carson is repeatedly described in these terms. She is actually called "unkempt" and "pitiful looking" by adults who see only her huge mass of impossibly curly black hair and her scroungy clothes. Her friend Martha thinks she is beautiful. At thirteen, she looks worse than ever by normal standards; she can sit on her long thick braid, wears no makeup and cannot afford to dress stylishly, nor does she particularly want to.
Live Action TV
In the U.S. remake of Shameless, Fiona skips the makeup, hairstyling, and even neglects to wear a bra on occasion: she still attracts at least half a dozen men over two seasons, even one woman. Emmy Rossum has said that she spends five minutes in the make-up trailer, just long enough to rub mascara around her eyes. She still manages to look like this
In Firefly, River Tam has long tangly hair, pale, unhealthy skin, bags under her eyes, and minimal makeup; this does not stop the fandom from adoring her, and several characters in-series remark upon her attractiveness. It helps that she's played by Summer Glau, see below.
On the same note, Firefly usually had Jewel Staite in homey overalls and occasionally covered in grease. As Simon says, Kaylee looks good especially covered in engine grease.
Dr. Gregory House has big bags underneath his eyes, Perma Stubble, and bed hair. His rugged, unkempt look is actually more attractive than the one and only time we see him clean shaven and smartly dressed. Too bad his personality flaws take away from it. Or not. Specifically a patient once said that Ashton Kutcher and House have the "same bedroom eyes."
Battlestar Galactica: Kara "Starbuck" Thrace wears no visible makeup, dresses in military-issue clothing, and is frequently seen bloody-faced, sweaty, and tired, with her golden hair either messed up or in a utilitarian, all-business ponytail.
Misha Collins as the angel Castiel in Supernatural. You'd think an angel with stubble, perpetual bedhead, rumpled tie, and hobo trenchcoat wouldn't be that attractive, but he is. In fact, some people have turned every aspect of his ruffled appearance into outright fetish fuel.
Summer from Power Rangers RPM. In flashbacks to her old life as a Rich Bitch she looks alright, all dolled up in a party dress and loads of make-up, but many will agree she's much hotter in her biker gear, with her hair loose and a little bit of dirt.
Most will agree that Kate (Evangeline Lily) from LOST looked far, FAR more attractive with scruffy clothes, messy hair and minimal makeup on the island than she did all done up on the mainland.
There were four women on Robin Hood and at least three of them looked much nicer when they were "roughed up" a bit. Marian (Lucy Griffiths) looked gorgeous when her hair was loose and her clothes unkempt, Djaq (Anjali Jay) made her Sweet Polly Oliver a true Bifauxnen and had many straight females questioning their preferences, and Isabella (Lara Pulver) was infinitely more beautiful with her hair wild and her Gorgeous Period Dress all askew. The aversion was Joanna Froggat as Kate, who was given two rather dreadful hairstyles (one which was known as "the forehead braid"), but who looked her best during the only scene in which she had to tie her hair up off her face, showing off her high cheekbones.
How I Met Your Mother: Robin qualifies. When trying to convince her not to move in with Ted, Barney asks her how she's going to feel when Ted sees her without makeup. She informs him that she's not wearing makeup right now. His response? "Holy crap, you're gorgeous!"
In an episode of The Fresh Prince of Bel-Air, Hilary's boyfriend Trevor comes over, finding her wearing baggy clothes, not wearing makeup and wearing her hair down. She's horrified that he's seeing her like this, but he's genuinely blown away by how attractive she looks. Then Jazz comes over and tells Hilary she could stand to fix herself up. Fortunately, we are meant to disagree with Jazz.
Shane from The L Word. Her hair was always a mess (this despite her being a hairdresser), she never wore makeup and dressed casually at best. And yet she never lacked for appreciation.
In the Mystery Science Theater 3000 short "Body Care and Grooming", we are presented with two versions of the same woman—first with her hair messy, her blouse wrinkled, her socks mismatched, etc.—and then cleaned up, prim and proper, Fifties-style. Although the makers of the short clearly mean the "clean" woman to be more attractive, Joel and the bots (Crow especially) prefer the "sloppy" woman. Regardless, the message is lost when it's clear that the actress was incredibly attractive either way.
The Doctor Who episode The Doctor's Wife features Idris, a beautiful woman who is a mess due to having fallen through a hole in space-time. She dies at the beginning of the episode and her body becomes host to the soul of the TARDIS.
In Gilmore Girls Lorelai and Paris have each said that they envy Rory for being able to wake up in the morning and look great.
Morgana and Guinevere play this out as part of their Hourglass Plot in Merlin. Guinevere starts out as very plain and gradually becomes Progressively Prettier, whilst Morgana is a perfectly-groomed lady who eventually ends up living in a hovel with dirty hair and dark makeup. Fan reaction varies wildly.
In the Canal + series "Borgia"(no, not the Show Time series The Borgias), the characters Lucrezia Borgia, Giulia Farnese, and Sancia Squillace(d'Aragona) are played by german/russian actress Isolda Dychauk, italian actress Marta Gastini, and czech actress Eliska Krenkova respectively. Since the series has actress in costume with either little or no make up at all, the actresses for these three characters are naturally quite pretty.
The Big Bang Theory has Penny as perfectly willing to chill at home in an oversized college football t-shirt and her hair messily pulled up. It's become a recurring joke that she KNOWS how to dress up and knock it out of the park when she wants to, she just chooses not to. This is more evident in later seasons, as the first few seasons had her mostly in fanservice heavy tank tops and short shorts. Although it was averted in an episode with her getting addicted to an MMORPG, as her hair got greasy and frayed and her skin blotchy.
In one episode of Scrubs Elliot runs to the hospital on her day off to get some advice from Turk without J.D. knowing she was there. Turk comments that she looks different and she remarks offhand she didn't bother putting any make-up on. It is subtle but a theme of the episode was that Character Development doesn't eliminate ALL of your issues, as while Elliot proved to still be neurotic there were previous episodes that had her obsessing over her appearance despite the fact she obviously didn't have to try so hard.
The No Doubt music video for '"Underneath It All" shows Gwen Stefani gradually wearing more "plain" clothing and makeup, becoming more attractive with each step.
Courtney Love in her heyday frequently wore tattered babydoll dresses and bright red lipstick in the vicinity of her mouth rather than on her mouth, and appeared to be completely unacquainted with the concept of hairbrushes. She cleans up occasionally now, but 'messy' is still her most iconic look.
Katiejane Garside of Daisy Chainsaw/Queen Adreena/Ruby Throat is an amazing exemplar of it . NSFW.
Implied about the girl sung about in "She Don't Know She's Beautiful" by Sammy Kershaw given that a lyric comments "Mornin' comes and her hair's all a mess. That's when she thinks she looks her worst. It's times like this she don't know why I can't take my eyes off her".
From other characters' dialogue in Neverwinter Nights 2, Elanee (being a druid) is constantly rather dirty, has never touched a comb/toothbrush in her life, and smells rather earthy.
In Amagami, Kaoru Tanamachi's most distinctive feature is her SEX HAIR, and many fans believe that she's much more appealing because of it.
From Yggdra Union, Gulcasa's knee-length hair is always rumpled-looking and flyaway—so much so that when character designers wanted to conceal his identity for the prequel, the most important alteration was his tying it back neatly in a ponytail. General consensus seems to be that he looks more mature (and more masculine) with it loose and messy.
In the same vein, fully groomed and dressed up, the Spoony One is at most only dorkishly handsome, but during most of his videos when he's looking slightly scruffy both his sexy and Moe count jumps up significantly.
MarzGurl as well, looks like she only occasionally combs her hair, and wears T-shirts that look like they might have just come out of the hamper.
He's nowhere as sexualized as the Critic or Ask That Guy, but Chester A. Bum still has Doug's big blue eyes and dimply smile, an accessible layer of dirt on his face, and the added bonus of being a WoobieKeet.
A lot of "Natural Nudes" websites go for this angle, exemplifying the unaltered beauty of the female form.
Widget of the Whateley Universe. She's very attractive, but she doesn't use makeup and she just slaps a bicycle cap over her hair, then jumps into baggy clothes and maybe a labcoat. She has a huge crush on Thunderbird, who thinks of her as a 'pal'.
Jessica from Season 2. Same unhealthy pale skin, dark circles and rumpled clothes, but many viewers found her quite attractive.
Hell, most protagonists in the mythos suit this trope (not to mention a few antagonists). It's become something of a running joke in the fandom that in order to star in a Slenderverse vlog, you must possess the kind of good looks that hold up under constant insomnia, Sanity Slippage and being splattered with blood.
Summer Glau certainly seems to have this trait, as she looks more attractive and beautiful without makeup. This is especially noticeable with her characters in The Sarah Connor Chronicles and is rather striking in Deadly Honeymoon, where there are scenes showing the characters without much makeup and later with it - and the difference is amazing. With the makeup, Summer looks like a doll, while without it, she looks very real and natural.
Truth in Television: Sometimes tabloids print photos of celebrities caught without makeup. The point of this is obvious; as pointed out in the header, the fashion industry wants us to think we all look like trolls without their products. A while back, a paparazzi caught a snapshot of Maggie Gyllenhaal coming home from some awards show. Apparently, even tired, disheveled, and (possibly) hung over, she's freaking gorgeous◊. She's most definitely wearing make up, though, and neither her hair nor her clothes are below average for any woman in public.
Marilyn Monroe once posed in a note form-fitting, tailored, with fringe on the bottom potato sack, just to prove to everyone what they already knew.
An apparently real candid shot of Marilyn without makeup was printed in the biography Goddess. She looked startlingly like Ingrid Bergman, and the caption "Lovelier without makeup" was entirely deserved.
Amanda Palmer wears wacky costumes onstage, but there's plenty of pictures of her completely dressed down. She looks extremely different without dark lipstick and eyeliner on, but she still looks quite beautiful. And her hair is always unkempt looking.
According to legend, Richard Burton proposed to Elizabeth Taylor after seeing her freshly awoken, without make-up and with pillow hair, and wearing a decidedly unsexy flannel pyjamas.
Helena Bonham-Carter seems nearly incapable of being a Kempt Beauty; any photo of her out of character will almost invariably have her hair looking just terrible.
Clive Owen's bed surely travels with him. He always seems to have awoken up five minutes ago, even when he kills mooks with carrots.
Mia Wasikowska, when her hair is long, anyway, looks like a real life River Tam. Her hair care routine seems to consist of two steps: 1. Wash it. 2. Maybe comb it.
Edward Furlong is this trope embodied. His hair is always long and messy, his clothes are always loose and he's partial to plaid flannel shirts and torn jeans, yet he's quite the Mr. Fanservice, especially in his youth.
Much of artist Phil Noto's work has this aesthetic, and he's cited 1960s pin-ups as a big influence on his style.
Many of Annie Leibovitz's photos are of people undressed or dressed down, particularly a series in the book Women, featuring Vegas showgirls in and out of costume.
Michelle Rodriguez has a sexy down to Earth tough girl look with little to no make-up. Seeing her in a dress and all dolled up is unnerving to say the least.
Invoked by the Powers That Be behind the Official Stargate Conventions when they started offering two options for photo ops with Michael Shanks: scruffy, unkempt Michael or the suavely dressed, shaven version.