At one point in Inio Asano's A Girl By The Sea, Isobe is shown wearing a pair of headphones with a very visible Sony logo.
Alice & Zoroku Episode 3 has a scene set in a Carl's Jr. restaurant, Episode 5 features a Snickers candy bar.
In Area 88, Makoto Shinjo uses Nikon cameras, and even makes a point to mention this in dialogue early on (which is accurate enough: Photography equipment can get rather expensive, and much of it is not compatible between brands, causing folks to get rather invested in a particular brand as they put money into lenses and flashes and what not.)
Basquash!, by its nature as a basketball-playing humongous mecha series, has a deal with Nike, to the point where a Nike logo is prominently displayed in the opening sequence.
Barcardi rum shows up in Black Lagoon during a drinking contest, and Dutch is shown using a Heineken can as an ashtray.
The manga also has a scene where Revy is hit in the face with a pint of Häagen-Dazs. This was Adapted Out of the anime version.
The fourth chapter of Bokura no Hentai has the three leads eating Häagen-Dazs ice cream together, complete with a close-up panel of the containers.
Cardfight!! Vanguard is a Merchandise-Driven series like many others, except for the fact that, while other shows have the characters just pull out new cards/powers/weapons and that's it, here you actually have in multiple occasions the characters stating that someone just played a new card that is available now in the newest set of booster packs, with the expansion set's name being said out loud. In particular:
During Aichi's first match in the National tournament in episode 17, he plays Gordon, Knight of Truth, with his opponent actually being shocked that he can already use properly a card that was released only some days ago.
A similar scene happens in episode 22 when Gouki rides King of Demonic Seas, Basskirk. Made more weird since almost every other unit he played before in that match comes from the same booster set as Basskirk.
Episode 25 is basically a huge advertising for the then-recent release of the Nova Grappler and Oracle Think Tank Trial Decks.
Episode 51 features a brief scene of a match between Emi and her friend: the latter plays a Neo Nectar deck, and at the end of the game she literally says that she played the new cards she just found in the new expansion set Awakening of Twin Bladesnote Which indeed is the set where the Neo Nectar clan was introduced.
In Cat Planet Cuties, the characters eat hamburgers with very prominent A&W logos visible on the wrappers.
Pizza Hut has a very lucrative deal with Code Geass: Lelouch of the Rebellion. While Humongous Mecha and Magical Eyes battle it out, Pizza Hut signs are in every episode and the cast eat pizza every chance they get. This gets slowly phased out over the course of the series, but one element sticks around up to the very last scene of the series: C.C.'s prized possession is a plush of Cheese-Kun, Pizza Hut's mascot in Japan. The Pizza Hut logos are censored out in the American release, perhaps because Pizza Hut U.S. wasn't too hot on the idea of sponsoring anime, nor one whose protagonist is a vengeance-minded terrorist. Cheese-Kun remains unedited, presumably because the only Americans who know what it is are Geass fans who watched the show subbed.
This is particularly impressive given that the show takes place in an alternate universe where the American Revolution failed and the Americas became the seat of a new absolutist British Empire after Napoleon kicked them out of the British Isles. Societies may change, civilizations may rise or fall, culture can vary radically, but evidently, Pizza Hut is the one eternal constant.
The series also had a somewhat strange placement of Soproni Kékfrankos, a Hungarian wine (even mentioned in dialog). While the name of the wine is completely correct right down to accent, the name of the producer and Hungary itself is a bit misspelled. Leaving us to wonder if it is a real Product Placement or just a particularly careful Bland-Name Product.
There are very prominent Biglobe logos (the leading Japanese ISP) where people are surfing the web. This wasn't translated in the dub and so flew right over the American's heads.
Darker Than Black features numerous advertisements for @Nifty, the ISP which originally streamed the episodes online. It also has the occasional Coca Cola logo as well. Like in several other series, Pizza Hut appears here and there (replaced by "Pizza Slice" in the English dub).
The computer through which L communicates in Death Note is a Mac, although the apple logo is never actually visible. Likewise, Light's computer isn't explicitly identified but is recognizable as a Mac G4. Since the series was set 20 Minutes into the Future, it's a bit out of date now.
Speaking of Biglobe, some (authentic looking!) computer screen closeups in the Digimon Adventuremovie show Koushiro very obviously using that particular ISP to get online.
In Season 2 of Durarara!!, Shizuo and Tom are shown eating at a Lotteria fast food restaurant.
In Eyeshield 21, Hiruma is usually seen toting around a laptop. In some places, it is revealed to be a Sony Vaio.
In an omake for the manga Fairy Tail there is, pretty bizarrely considering this is an entirely Fantasy Constructed World, a blatant part of product placement at the end where Grey hands the two of them a bottle of Coca-Cola. Yeah, it's just weird.
The anime OVA was sponsored by Nissin Foods as part of an anniversary promotion — and apparently the only food available to the colonists on the moon is Cup Noodles.
When the action shifts to post-apocalyptic Earth, the only food available there is Cup Noodles too... but they have Seafood flavor! This leads to some serious Fridge Logic: are the people on Earth eating 200 year old Cup Noodles? If not, are there Nissin factories still operating on Earth even though everyone's dirt-poor? Since the dystopian government on the Moon is trying to uphold the Masquerade that everyone on Earth is dead, do the Earth and Moon branches of Nissin have any contact with each other? Or is Nissin part of the whole conspiracy in the first place?
Most of the clothes in The Garden of Words are from real brands, with a Fila jacket making a visible appearance.
Ghost in the Shell: Arise has advertisements for Microsoft Surface tablets, as well as a few appearances from the device itself.
Sunrise makes the list again. The Girl Who Leapt Through Space had logos of its toy and music companies flying by in the first few episodes, but then comes episode 14. There's a long scene of Nina, Bou and Min eating at a Pizza Hut, with the logo in the dead center of the screen.
Episode 7 of Girls Bravo actually has a Honda motorcycle show as a plot point.
At one point in the movie, a computer boots up and we get a few good seconds devoted to the startup screen for Windows 95. They even used the Windows 95 startup noise. See for yourself.
Not only Windows 95, but the computer's blatantly a NEC PowerMate (for the uninitiated, NEC was the creator of the Turbo-Grafx 16, and it's semiconductor business fabricated CPUs for Sega back in the 32x, Saturn and Dreamcast days). They also made desktop computers and notebooks up until recently, when they decided to discontinue these to focus on the server and supercomputing sector.
In the first episode of Haiyore! Nyarko-san, Nyarko drags Mahiro to a bookstore where several manga and light novels published by GA Bunko (who publishes Nyarko-san itself) show up. You can also see posters advertising Nyarko-san, specifically its anime adaptation — which you're currently watching.
Battle Tendency ends with Joseph noting that despite his dislike of the Japanese, he's still happy to own a Sony Walkman (shortly followed by a close-up of it).
In Stardust Crusaders, while Jotaro has himself locked up in prison, he uses his Stand to swipe various items to keep in his cell, including a copy of Shonen Jump (which JoJo was published in at the time).
Also in Part 4, Reimi Sugimoto uses sticks of Pocky as part of a fortune-telling game. There's even a shot of the box and logo.
In K-On!, the girls use real, licensed instruments from Gibson (Yui), Fender (Azusa, Mio, and their amps), Yamaha/Zildjian (Ritsu), and Korg (Tsumugi). Sawako also owns a Gibson Flying-V and at one time had a Gibson SG.
A couple of the Kara no Kyoukai movies prominently feature Haagen-Dazs strawberry ice cream, even tying it into the character development.
Pizza Hut sponsored it, complete with official art of the cast enjoying some delicious pizza. Nana Mizuki, Fate's voice actress, even ordered a delivery just to collect a limited time offer special pizza box... with Fate Testarossa on the cover.
A scene in has Nanoha, Alyssa, and Suzuka playing a generic JRPG, before switching it out for a few rounds of Wii Sports. It was Tennis, for those wondering.
When Negi's party was scattered during Magic World arc, one of the few things that Chisame was able to bring with her was a CalorieMate Block she put in her robe.
An in-story example: During the Battle of Mahora, (which almost all the students think is just a game), Chao, the arc's Big Bad pops up on the giant screens to do some Evil Gloating. After which she does an ad for the restaurant she manages.
And Pizza Hut strikes again in the 4th season of Maria-sama ga Miteru, where the logo is often prominently displayed in the background, even in an amusement park.
An episode of Nichijou contains a joke where the punchline involves Hakase encouraging Nano to bring along a Snickers bar as a snack in school.
Yamaha is one of the main sponsors of Nodame Cantabile. Consequently, every piano in that show is a Yamaha and melodicas are referred to as "pianicas".
Ouran High School Host Club not only uses Bland Name Products (most of which are seen in the anime), but in the manga we see Kyouya using an Apple computer with the proper OS displayed on the screen. He even has a few recognizable icons such as Skype.
In the anime, James occasionally has a set of reference cards if Team Rocket happens upon a new Pokémon. When 4Kids still had the dub of the anime, they'd sometimes cut these scenes out because of potential advertisement for the Pokémon TCG. Sometimes they would just remove the borders on the cards to make them look less like the real world TCG cards.
While on the topic of the 4Kids dub, this kind of editing got really stupid in the Advanced Generation. Most any things which had a picture of a Poké Ball on them were painted out (the ones on Ash's Hoenn Badge case and May's Ribbon cases were turned into red stripes). Oddly enough, this only seemed to happen in the US/Kids WB! airings; most international dubs didn't feature that censorship.
However, there's an even bigger product placement in two Sinnoh episodes—one has Meowth use a Wii Remote, and the other the Nunchuck attachment!
While the original TV series was very big on Brand X products, the Rebuild movies often have shot-for-shot recreations of scenes from the show. So scenes that originally had generic pizza boxes and soda cans in the background now have Pizza Hut and Pepsi logos plastered everywhere.
Also Doritos, Yebisu beer (not Yebichu), and UCC Coffee (whew!). Most of these have accompanying packaging advertising the movie as well.
In the second movie, there is a Lawson Convenience Store inside Nerv Headquarters. Asuka also uses a WonderSwan-brand handheld gaming console.
The third movie mostly averts this, except for Kaworu's piano, which is made by Yamaha. There's even a lingering shot where we clearly see the logo.
The Christmas Episode in volume 3 of Sgt. Frog featured Keroro using the "Yahoo!" search engine. The logo was even seen in the panel.
At the beginning of Spirited Away, a bag with "KINOKUNIYA", the name of a Japanese bookstore, written on it can be seen on it in the car Chihiro and her family travel in.
Fuji Television gets referenced a lot in Tokyo Magnitude 8.0 but it's perfectly sensible considering it's news and as an earthquake happened the characters are often viewing it. It's still suspicious how Yuuki has a "Fuji Staff" sticker on his backpack.
In Yotsuba&!, Torako uses a Nikon camera. The logo is even prominently displayed the first time she shows the device to Yotsuba.
In Chapter 88, Yotsuba's grandma reveals that she recently bought an iPhone, which she proudly displays. She then urges her son to get one too so she can use FaceTime with her granddaughter.
Apparently the only piano manufacturer in Your Lie in April universe is Steinway & Sons.
Mai Kujaku (Mai Valentine in the English versions) drinks Pepsi in one episode of Yu-Gi-Oh!. The reference was taken out in the American version. Starbucks coffee has also appeared. Many cards in Yu-Gi-Oh also happen to be shameless promotions for Konami games (Konami owns the rights to Yu-Gi-Oh) such as Castlevania, Gradius, Contra and even Metal Gear Solid.
The most recent translation, by Viz comics, of Read or Die had Yomiko using Jumpin battle (and pausing to read them). It was hard to read the katakana, though, so it might have been Jump, or possibly Corocoro Comics, a rival.
Superheroes have become a major entertainment industry in Tiger & Bunny, and the heroes themselves are covered in advertisements for real-life products. There's even a commercial spot for Pepsi NEX featuring Blue Rose which blurs the line between Ad Bumper and ad. On the other hand, several characters are represented by fictional companies. The characters get yelled at fairly frequently by their sponsors for causing collateral damage (which the sponsors pay for) and get criticized for heroics off the air as it means they don't get any advertisement time.