This list is by no means complete, and only includes magazines that we feel comfortable enough with to accurately review. There's a lot out there, so don't limit yourself by what you see! You can find a manga series on nearly every imaginable topic, have fun with it.
target audience: School-age boys
content: A wide variety of action and adventure series, from "Fighting Schoolboy Shounens" (featuring middle-school students with special powers or martial arts abilities) to Mecha series (giant futuristic robots) and pretty much anything with a video game tie-in.
Magazines: Anything with "Shounen", "Jump", or "Young" in the title is a Shounen magazine. The king of them all is naturally Young Shounen Jump, which is currently being released in America as well. These books rarely have objectionable content and are heavy on speedlines and fight sequences, and the language is typically easy for beginning students to catch onto.
Gakuen specifics: Shounens aren't our specialty, of course, but that doesn't mean that Flame of Recca (a Shounen Sunday publication) isn't filling up a shelf in my bedroom, just like half the preteen boys in Japan. So check a shounen out every now and then, you may be surprised by what you find! For the slightly-older set, there's Shounen Ace, which carries some deeper cerebral works like Evangelion and MPD Psycho, far more appropriate for high-school and up than the youngsters. Then one step above that is Young Magazine, aimed more at young twenty-somethings. Young has had some extremely successful long-running series, including 3x3 Eyes, Initial D, Bebop High School, and Chobits.
target audience: School-age girls
content: Magical transforming girls, sweet first-love romances, saving the world from evil or just trying to pass the exams to get into high school.
Magazines: Cuteness ahoy! Shoujo stories are typically heavy on character development and often feature everyday situations with a twist. Worried about your school festival? Well, it surely couldn't go as badly as it did for [insert any lead character here]!
Nakayoshi: Probably the cutest of the cute, Nakayoshi is the home of Sailor Moon and Card Captor Sakura and a host of other series where cute girls transform into even cuter outfits and save their families/town/boyfriends.
Ribon: A popular book for young girls with lots of young romance and trendy fashion. Big names include GALS!, Marmalade Boy, and Kamikaze Kaitou Jeanne. Has a large English-speaking internet following, if you need translation help.
Margaret: To be honest, Margaret kind of mystifies us. It's aimed at middle-schoolers, yet it's the home of one of the longest-running dark angst-ridden Boy's Love stories, Bronze. ...? But you'll also find works like Hana Yori Dango. The art style in Margaret is generally less "bubbly" and cutesy than Ribon and the like.
Flower: Romance comics for older girls, published in the magazine "Sho-comi". Famous works include Fushigi Yuugi, Tokyo Juliet, and Princess Army.
Hana to Yume: More mature themes than you'll find in the others, but still a shoujo book. Ironically, Hanayume's most unusual and unexpected works have been the most popular, such as Yami no Matsuei and Angel Sanctuary. More typical for the book include Fruits Basket, Hanazakari no Kimitachi he, and Koucha Ouji.
Princess: Coupled with Bonita comics, these titles cover a fair amount of historical and fantasy settings as well as shoujo horror titles like Vampire Princess Miyu.
Kimi to Boku: Sony's foray into comics for girls, it's somewhere on the borderline between standard shoujo and Ladies. It includes titles like Gravitation involving shounen-ai, and series that skirt the issue like Z/ETA and Raideen.
target audience: Anyone, varies by specific book
content: Typically the best-known series to foreign fans thanks to anime tie-ins, these books generally bridge the gap between genders through exciting action, strong characterization, and humor. Books you wouldn't be embarrassed to read on the subway.
Magazines: This category is our catch-all, so it's less cohesive in terms of content. While you can technically force these books into shoujo vs shounen, the audience isn't so clearly defined.
Kadokawa: Hugely popular titles destined for TV series, from a huge super-conglomerate publisher. They're responsible for Newtype as well, and a whole host of books fall under their umbrella; just look for the phoenix on the spine. But the "general" titles include fantasy like The Slayers in "Dragon Magazine", horror like Anne Freaks, and entire books devoted to Gundam. Their books have high production values and are usually top-notch manga.
Enix: Familiar in the states for their video games, Enix covers a lot of ground. The "Gangan" magazines focus on shounen works (that girls enjoy too) like Star Ocean, Violinist of Hameln, and Papuwa-kun. "G-Fantasy" is a crossover magazine with high-energy series for all audiences, like Gensomaden Saiyuki, E'S, and Fire Emblem. "Stencil" magazine is oriented towards a female audience, with more Enix fantasy but even greater emphasis on characterization and sweet romance.
Eyes: Delegated to the "other" category because it has died, Eyes was an influential primarily shoujo book and shall be missed. The titles were aimed at older teens, with lush settings and often fantasy-driven stories. Some unique and memorable works came out of Eyes, such as Gorgeous Carat and Alichino.
Asuka Comics: A subset of Kadokawa aimed technically at women, Asuka publishes popular series in a variety of magazines. Asuka Magazine features titles like D*N*Angel and X, while Asuka DX is for an older audience, with more mature themes in series such as Seimaden. Fantasy DX is home to Angelique and Cowboy Bebop, and Mystery DX seems to focus on romance stories like Wish and Higuri You's Ludwig II. Asuka Ciel and CL-DX are really more Ladies comics, which kicks us into the next section.
target audience: Adult women, age varying by specific magazine
content: Boy's Love in every imaginable setting and context. Shoujo series almost exclusively feature female lead characters; Ladies is the exact opposite (whether or not BL is involved.)
Magazines: If you see two boys snuggling on the cover, it's a Ladies. Heck, if a boy is on the cover and he's not killing something, it's probably a Ladies. BL in shoujo works is usually understated and hidden between the lines in nuances and subtext; Ladies doesn't hold back. Some books are appropriate for high-school aged girls; some are absolutely not. Descriptions follow.
Asuka Comics CL-DX: One step up from Asuka DX, the stories are extremely tame and sweet BL, or at least highly suggestive to that end. The content is not objectionable and usually limited to nervously holding hands at night in the park.
Wings: A well-established collection of works for adult women bordering on pretentious, Wings is as adept at fantasy as they are at telling everyday stories. CLAMP's RG Veda and Tokyo Babylon ran there, as well as many classics like Earthian.
Chara: Great BL stories that you can share with your teenage daughter, Chara has a ton of talented artists with stories based on characterization and relationships. The titles are generally mature, but explicit material is rarely allowed. If you're looking into a particular artist, a Chara series is a safe bet. Big titles include Utsukushii Otoko and Yatteranneeze.
Gust: The Indies Rock Band of Boy's Love, Gust publishes some unusual series from lesser-known artists. The works can be quite explicit and the art isn't always great, but the stories are packed full of emotion. The home of Fish in the Trap and Boku no Suki na Sensei.
Biblos: All Boy's Love, all the time. Many great artists, working in a variety of magazines:
BeXBoy (BBC): The headline magazine, with Boy's Love stories of all types. Generally somewhat explicit, but can be completely innocuous at times. Just right for the taste of many Ladies' fans; not too hot, not too cold.
Zero Magazine: The least explicit of the Biblos line-up. Zero runs stories suitable for older teenagers as well as the typical Biblos audience.
BeXBoy Gold (SBBC): On the other end of the spectrum, Gold is generally explicit and often includes more taboo subjects than would be found in the other magazines, such as Shouta stories and incest. There is a fair amount of crossover with BeXBoy in terms of content, though, as some squeaky-clean stories have shown up in Gold, and vice versa. Some artists, based upon prior works, will be relegated to Gold automatically regardless of the nature of their current work.
Zips (now called "Luv"): A unique book somewhere between a monthly "phonebook" manga installment and a tankouban, Zips are a collection of short works by many mangaka with a general theme, such as "Celebrities", "Newlyweds", or "Teachers". Zips are an excellent way to meet new artists in Boy's Love, and decide if you are interested in their storytelling or art style. There's always at least one story we adore, and one story we just hate, but either way it's a learning experience. Regardless of topic, the books include some explicit material.