Updated September 2014. New ones, updated ones and ones still to be done in bold.
ANA – All Nippon Airlines
Asahi – Morning light
Benihana – 紅花 – literally “dark red flower”, though I have a feeling it’s actually the name of a specific flower
Bridgestone — named after founder Shojiro Ishibashi. The surname Ishibashi (石橋) means “stone bridge”.
Canon — Originally (1933) Precision Optical Instruments Laboratory. The new name (1935) derived from the name of the company’s first camera, the Kwanon, in turn named after the Japanese name of the Buddhist bodhisattva of mercy. (In Japanese it is still always pronounced with the first sounds as kya- kyanon – like the religious figure)
Casio — from the name of its founder, Kashio Tadao, who had set up the company Kashio Seisakujo as a subcontractor factory. (In Japanese it is usually pronounced with sh sound- Cashio- as the sounds si and shi are indistinguishable in Japanese).
Daihatsu — shortened from 大阪の発動機製造 Osaka motor production and it got shortened to 大発 – Daihatsu (Great development), as dai is another pronunciation for the O in Osaka (thanks to the commenter below for this one)
Daiichi Sankyo –第一三共 – the kanji seem to mean something like “Number one from a combination of three”
Daiwa – another pronunciation of Yamato (大和), an ancient name for Japan.
Datsun — first called DAT, from the initials of its financiers Den, Aoyama and Takeuchi. Soon changed to DATSON to imply a smaller version of their original car, then (as SON can means “loss” in Japanese) again to DATSUN when they were acquired by Nissan.
Denon – “The Denon brand came from a merger of Denki Onkyo and others in 1939.” (presumably actually “denki onkyou” – 電気音響 – meaning “electronic acoustics”)
Dentsu – “Electronic communication” (電通) because it used to be a telegraph company
DHC – short for “daigaku honyaku sentaa” (大学翻訳センター), meaning “university translation centre” as that is what it started as, despite being better known for cosmetics nowadays
DNP – Dai Nippon Printing, still usually known as Dai Nippon Insatsu (大日本印刷) in Japanese. Dai Nippon is mainly a colonial hangover name meaning “greater Japan”, but not sure in this company’s case.
Doutor – apparently from the Portuguese name for “doctor” after a trip to that country by the founder, but have neither been able to trace the source of that story nor work out the connection he thought there was to coffee
Duskin – A few explanations in Japanese here http://ja.wikipedia.org/wiki/%E3%83%80%E3%82%B9%E3%82%AD%E3%83%B3 but the most likely seems to be the beginning of the English expression “dust cloth” with the end of the similar Japanese expression “zoukin”, as just the Japanese word was a bit too direct and unattractive (just noticed that a commenter beat me to this)
Ebisu – Originally “Yebisu”, both versions being names of a Japanese God, part of the seven who are often pictured together. The name of the area in Tokyo comes from the beer company rather than vice versa. Thanks to a commenter below for beating me to this one.
Epson — Epson Seiko Corporation, the Japanese printer and peripheral manufacturer, was named from “Son of Electronic Printer”
Fujitsu – Short for Fuji Tsūshinki Seizō (富士通信機製造 - Fuji – after the mountain – telecommunications equipment manufacturing)
Hakuhodo – 博報堂 – has kanji from museum, information and temple, will try and research why soon…
Hard Off- It is a second hand hardware store in the same chain as Book Off (“off” suggesting cheapness), but not a chain that will be expanding abroad unless it takes a huge change in product range, I think…
Hitachi — old place name, literally “sunrise”
Honda — from the family name of its founder, Soichiro Honda (Honda is a common name, with the first kanji “Hon” meaning root or base, and the second kanji “da” meaning rice field).
Isetan ― 伊勢丹
Isuzu – Always written in Hiragana as いすゞ, with the final symbol simply meaning “repeat the last symbol with voiced”. My computer brings up the kanji 五十鈴, which would mean “fifty bells” and looks like a place name
JAL — from Japan Airlines
JCB credit cards
JR – Japan Railways
JVC — Japan Victor Company
Kaldi – the name of the goatherd who was supposed to have first discovered coffee
Kanebo – Always written in katakana, so can’t find the original meaning 鐘紡
Kao – 花王 – Literal meaning of the kanji is “flower king”, but that is apparently a name for the botan flower. The pun with the word for face “kao” is apparently deliberate. (Thanks to commenter below for this additional info)
Kawasaki — from the name of its founder, Shozo Kawasaki. Kawasaki is a very common family name that comes from the kanji “Kawa” meaning river and “saki” meaning cape (which explains why Kawasaki the company has no connection to Kawasaki the much ignored city between Yokohama and Tokyo).
Kirin – Giraffe, and the mythical Chinese creature which shares its name.
Komatsu — Japanese construction vehicle manufacturer named from the city of Komatsu, Ishikawa, where it was founded in 1917.
Konica — it was earlier known as Konishiroku Kogaku. Konishiroku in turn is the short for Konishiya Rokubeiten which was the first name of the company established by Rokusaburo Sugiura in the 1850s
Korg — named from the surnames of the founders, Tsutomu Katoh and Tadashi Osanai, combined with the letters “rg” from the word organ.
Kumon – 公文 ????
Kyocera — from Kyoto Ceramics, after Kyoto in Japan.
Marubeni – 丸紅 – literal meaning of the kanji is “circle” + “dark red/ crimson”, which looks like a family name to me
Maruetsu – マルエツ – doesn’t seem to be any kanji for it, so not sure the meaning or where it comes from, maybe an abbreviation of two names or a longer company name
Matsuya – 松屋 – simply means “Shop of Mr Fir Tree”, hence being used for completely different and unconnected companies such as a gyudon beef bowl restaurants and a posh department store
Mazda Motor Corporation — the company was founded as Toyo Kogyo, started manufacturing Mazda brand cars in 1931, and changed its name to Mazda in 1984. The cars were supposedly named after Ahura Mazda, the chief deity of the Zoroastrians, though many think this explanation was created after the fact, to cover up what is simply a poor anglicized version of the founders name, Jujiro Matsuda. This theory is supported by the fact that the company is referred to only as “Matsuda” in Japan (松田 – fir tree and rice paddy, a fairly common name).
Mitsubishi — 三菱 – the name Mitsubishi has two parts: mitsu means three and hishi (changing to bishi in the middle of the word) means diamond (the shape). Hence, the three diamond logo. (Note that “diamond” in this context refers only to the rhombus shape, not to the precious gem.)
Mitsui – 三井 – Three wells, a place name and family name
Mitsukoshi – 三越
Mizuho – 瑞穂 - abundant rice, from an ancient name for Japan “豊葦原の瑞穂の国 (とよあしはらのみずほのくに)’ Toyoashihara no mizuho no kuni’.
Mos Burger – Mountain Ocean Sky, apparently
MUFG – Mitsubishi UFJ Financial Group
Muji – usually known in Japanese as “mujirushi”, short for “Mujirushi-ryouhin” (無印 – good quality without branding – ironically for what has become an expensive and trendy brand).
NEC – Nippon Electric Company
NHK – Short for Nippon Housou Kyoukai (ニッポン放送協会) Japan Broadcasting Organisation).
Nikkei – (日経) short for Nihon Keizai Shimbun (日本経済新聞 – Japan Economics Newspaper)
Nikon — the original name was Nippon Kogaku, meaning “Japanese Optical”. There is still a “Kogaku street” 光学通り in Ooimachi, Tokyo to one of their factories.
Nintendo – 任天堂 – According to a book on the company, the word “Nintendo” means “leave luck to heaven” or “We do what we can” which suggests the chance inherent in card games, their first products.
Nissan — the company was earlier known by the name Nippon Sangyo (日本産業) which means “Japanese industry”, making the kanji 日産
Nissin – 日清, which looks like it might mean “Japanese pickles” but apparently is short for the motto “日々清らかに豊かな味をつくる”, “Making a clean and great taste every day.”
Nomura – 野村 – A common family name meaning “field village”
NTT – Nippon Telegraph and Telephone
NTT docomo – Do communication????
Odakyu – 小田急 – I’m guessing it’s short for Odawara Kyukou from the city where it goes
Resona – りそな – ???? (strange as it’s pronounced risona with ri as if it’s an English word, but written in hiragana as if it’s a Japanese word)
Ricoh – Short for Riken Kankoshi（利権感光紙Riken Sensitised Paper）, which would make the kanji 利光
Sansui – 山水 – mountain + water
Sanyo — 三洋 – three + oceans, not sure why
Secom – “security communication” (thanks to a commenter below)
SEGA — Service Games of Japan was founded by Marty Bromley (an American) to import pinball games to Japan for use on American military bases.
Seibu – 西武
Seiko —from Seikosha (精工舎), roughly “House of Exquisite Workmanship”
Seiyu 西友 – the kanji literally mean “West” and “friend”. The “sei” bit comes from Seibu as it’s the same group.
Sharp — Japanese consumer electronics company named from its first product, an ever-sharp pencil (mechanical pencil/ automatic pencil), still called “sharp pen” in Japanese after that product.
Shimano – a fairly common Japanese family name meaning “island + field” (島野)
Shinseido – 資生堂 – “The name ‘Shiseido’ comes from Chinese Yi Jing, the Book of Changes from the Four Books and Five Classics of Confucianism.” according to their website, but doesn’t explain why or what it means
SMBC – Mitsui Sumitomo Banking Corporation (no idea why the first two words are reversed in the acronym) – thanks to a commenter for a correction
Sony — from the Latin word ‘sonus’ meaning sound, and ‘sonny’ a slang word used by Americans to refer to a bright youngster, “since we were sonny boys working in sound and vision”, said Akio Morita. The company was founded as Tokyo Tsoshiu Kogyo KK (Tokyo Telecommunications Engineering Corporation) in 1946, and changed its name to Sony in 1958. Sony was chosen as it could be pronounced easily in many languages.
Subaru — from the Japanese name for the constellation known to Westerners as Pleiades or the Seven Sisters. Subaru was formed from a merger of seven other companies, and the constellation is featured on the company’s logo.
Sumitomo – 住友 – A fairly common family name whose kanji mean “live” and “friend”. “The Sumitomo group traces its roots to a bookshop in Kyoto founded circa 1615 by a former Buddhist priest, Masatomo Sumitomo.”
Sunkus – サンカス – Supposed to be the Japanese pronunciation of “Thanks”, although the Japanese only really use “Sankyu” for “Thank you”. A commenter quotes Wikipedia as saying the logo is “sun”+”kids”+”us” and so it’s also a pun on “sun”.
Suntory – Japanese pronunciation is actually “santory” (サントリ), although there is no difference between that and “suntory” in Japanese
Suzuki — from the name of its founder, Michio Suzuki. Suzuki is the most popular Japanese family name and means “bell tree”.
Takara Tomy – Always assumed this was from a merger of two companies, but my computer brings up the kanji 高良登美
TDK – Tokyo Denki Kagaku Kokyo 東京電気化学故郷 (Tokyo Electric Chemicals – have no idea what the last two kanji mean)
Tokyu – Short for Toukyou Kyukou (東京急行) – Tokyo Express, the latter word being a usual part of train companies, which how Tokyu group started
Toray pronounced “torei”
Toshiba – 東芝 – It looks like “East lawn/ meadow”, but it’s a combination of the first syllable of Tokyo and the first word of “Shiba ura” (芝浦 – an area in Tokyo), from the names of the two companies that merged to create that company. The Japanese pronunciation is Toushiba with a long first syllable, like Toukyou for Tokyo.
Toto – 東陶 – the kanji for “East” and “ceramics”, I imagine the first of which comes from the first kanji of Tokyo (東京). The Japanese pronunciation has long vowel sounds – Toutou.
Toyota — from the name of the founder, Sakichi Toyoda (豊田). Initially called Toyeda, it was changed after a contest for a better-sounding name. The new name was written in katakana with eight strokes, a number that is considered lucky in Japan.
Tsutaya – 蔦屋 – “the shop of Tsuya/ Tsuya’s place”, but not sure yet what that kanji means, must be some kind of name and seems to mean some kind of a bird
Uniqlo – I seem to remember reading that it means “unique clothing company”
Wagamama – this restaurant chain called “selfish” (a word as negative in Japanese as it is in English) is, unsurprisingly, not a Japanese company.
Yakult – ヤクルト – from the Esperanto word for yoghurt (thanks to a commenter for this one)
Yamaha – a fairly common family name meaning “mountain + wing” (山羽)
Yamato – 大和 – An old name for Japan, also pronounced “Daiwa” (see above)
Yoshinoya – 吉野家 – The shop of Yoshino (吉野), a very common family name