Most manga are first printed in small sections in magazines. These magazines are generally fairly large, and contain several stories (sometimes as few as 5 or 6, but as many as 30). Due to their size, they're often referred to as "phone-book manga". They usually come out on either a weekly, biweekly, monthly or bimonthly basis. Occasionally some of the printers have "specials" (like Ribon has a winter-vacation special), or are printed on other, more irregular basis'. Most of these comics have a few colored pages on nice paper, and then the rest are on newspaper.
Most magazines are aimed at a particular audience, and they have themes, such as shoujo (Margaret, Ribon, ShoComics), shounen (Shounen Jump, Shounen Sunday), shounen-ai (Petite Flower), etc.. Sometimes, though, they're not very clear-cut. For example, Wings has some very shoujo stories like Earthian, but many of the series it runs have a more shounen feel. The comics that generally sell the best are shounen comics, and Shounen Jump is consistently on top. This is mostly because the majority of readers are male, but also because although the main focus of the stories are on action and male-oriented themes, they often appeal to both sexes. Rumiko Takahashi (her works are published in Shounen Sunday), for example, sells consistently well with both groups.
Once a certain amount of chapters has been finished, they start to be published in individual books, usually refered to as tankoubans. They're generally the size of a novel, and are about 180 pages. Aside from a color cover, they rarely have any color on the inside pages. They are sold divided first into shoujo and shounen sections, and then by subsections of major publishing houses, as opposed to dividing into the individual magazine titles. For example, if you looked in a shoujo section, there are usually two sections, Margaret and Ribon, right next to each other. Margaret and Ribon are both subdivisions of Shueisha, and Margaret is for all comics that were printed in any of Shueisha's high school-age shoujo magazines, and Ribon for anything printed in Shueisha's elementary school-age shoujo magazines.
Certain publishing houses, comics and individual sub-sections are known for certain types of stories. Since I don't generally read shounen, I honestly cannot make a big distinction between the printers. But I'll try my best. Since my purpose in doing this is mostly for people interested in buying tankoubans, I do not list these in terms of magazines, but rather the actual section they are put under.
Shounen Jump: Aimed at older boys and young teenagers, although people of both sexes and all age groups read it. Stories are usually action-oriented, and can have any sort of theme. Famous past stories have included Rurouni Kenshin and Yuu Yuu Hakusho.
Shounen Sunday: Aimed at older boys and young teenagers, although people of both sexes and all age groups read it. Stories are usually action-oriented, and can have any sort of theme. Famous past stories have included basically everything by Rumiko Takahashi (Ranma 1/2, Inu Yasha).
Margaret (Shueisha): Aimed at female junior high and high school students. Series tend to be somewhat mature, with no sex. It's where all of the different magazines with Margaret in the title are put. Most of the stories tend to be high school shoujo romances, but there are several fantasies and the shounen-ai series, such as Ryou and Bronze. Other famous series include Hana Yori Dango.
Ribon (Shueisha): Aimed at upper elementary girls, usually around the 4th to 6th grade. Most of the stories are sweet shoujo series, and tend to be in a elementary or junior high setting. Usually no shounen-ai/etc., although there have been a few unsual series running. Although there are some fantasy series running, there usually aren't that many. Some of the well-known series are Hime-Chan No Ribon, Kodomo No Omocha and Marmalade Boy.
Hana To Yume (Hakuensha): Aimed at junior and senior high school girls. Hana To Yume is the collective section for LaLa and Hana To Yume magazines. Hana To Yume tends to be known for being literally anything-goes, although most of the series well known in America are really their science-fiction ones, like Angel Sanctuary. They print anything from the classic Garasu No Kamen to newer titles like the Shingo To Kumiko Shiirizu. Hana To Yume titles are personal favorites of mine.
Flower (Shogakkan): This is the collective for mmmannny magazines, including the shoujo-etchi ShoComics. As such, it ranges from anything like My Darling Raion (which does have all-out sex), to Mizuiro Jidai (a sweet elementary school story). Most of the well-known Flower series, however, to tend to lean towards the more etchi sides. To those who are a little worried, rest assured that there are non-etchi series there (most of them aren't etchi), and Flower has a lot of very quality comics.
Kodansya (Kodansya): Another collective for a huge amount of magazines. Kodansya has many mature comics (they tend to be about the same maturity as Margaret -- the major thing is that Kodansya has a few women's magazines), like Mars, but it's probably better known for the series run under Nakayoshi like Sailor Moon. Nakayoshi is the only magazine that really presents much competition (as far as selling) for Ribon in the shoujo field, and it tends to have more mahou shoujo/idol stories than Ribon does.