Names and Honorifics

[Uesugi Norimasa]

Japanese names, like other East Asian names, use the "Eastern order", in which one's surname is placed before one's given name. Middle names aren't used. They are generally written in kanji, but some make use of kana.
This can complicate the reading of names (including place-names), in that there are thousands of kanji characters, some of which have the same pronunciation, and some characters can have multiple meanings or pronunciations. Therefore, a written name may have several pronunciations (some more common than others), but only one of which would be correct for a particular individual. For example "曄子" can be read as either "Akiko" or "Hanako". Likewise, most names are able to be written several different ways (some more common than others), with only one being correct for a certain individual. For example "Hanako" can be written as "曄子", as in the above example, but it can also be written "丹奈" or "花子".
Between the spoken and written forms of the name there can be multiple layers to the meaning, and puns/wordplay is not uncommon (the Japanese language as a whole is rich with puns/wordplay potential). Of course, the meaning of a name can sometimes be difficult to determine without first knowing the written characters, and furigana can be used to help determine the correct pronunciation.

Historically, commoners did not generally possess surnames until the Meiji Restoration in the 19th century, well after this forum's setting. When it was necessary for identification, they would often substitute their birthplace and/or lineage. For example, "Heisuke, from Taiwa Village/Mutsu Province" or "Heisuke, son of Takahiro". Alternately, an artisan or merchant could be named after their brand or product, or a craftsman after their profession.
Interestingly enough, members of the imperial family did not bear surnames either. If a member of the imperial family became a noble or commoner, the emperor would grant them a surname.
The upper classes, such as samurai or kuge (court nobles), did have surnames, which were often clan names. Throughout his life, a samurai/noble might have several names. The first of these is their childhood name, given to them at birth. These could be chosen to sound grandiose or lucky, or simply by fancy. Takeda Shingen's childhood name, Katsuchiyo, meant "1000 Victories in Succession". During their coming of age ceremony, they would be granted their adult name. Often one of the kanji characters would be hereditary, usually a part of their father's name. It was also possible for higher ranking personages to 'gift' one of the characters in their name. Later in life a samurai (especially higher ranking ones) might change their name for other reasons, such as to mark an important victory, fortuitous event, or change in allegiance. Many samurai, including daimyo, took a religious Buddhist name as well (some where, of course, more pious than others). A samurai could also be addressed based on their position, and the higher ranking land-owners were sometimes known by the lands they held. Lastly, some samurai/nobles were granted posthumous names upon their death.

How a name is used in speech often depends on the relationship between speakers. It is considered rude to refer to someone without any kind of honorifics (see next post), exceptions being close friends/family or where the speaker is older/superior to the person being addressed. If they possess a surname, it is impolite to address a person by their given name (again, with the exception of friends/family or superiors).
Typically ones superiors and seniors will be addressed without using their name at all, substituting their title instead (sensei ["teacher"], otosan ["father"], sesshō ["regent"], etc.).
Using another's surname without any honorifics can be considered rude, even in informal settings. Likewise, pronouns are used little, and can be considered disrespectful or too impersonal. Even when conversing face-to-face, Japanese often refer to one another by name, title, or honorific.

Common endings for Japanese names include:

Male: -aki, -fumi, -go, -haru, -hei, -hiko, -hisa, -hide, -hiro, -ji, -kazu, -ki, -ma, -masa, -michi, -mitsu, -nari, -nobu, -nori, -o, -ro, -shi, -shige, -suke, -ta, -taka, -to, -toshi, -tomo, -ya, -zou

Female: -a, -chi, -e, -ho, -i, -ka, -ki, -ko, -mi, -na, -no, -o, -ri, -sa, -ya, -yo

For more detail on samurai naming customs, see here.
For more detail on Japanese names in general, see here.

[Uesugi Norimasa]

The Japanese languages contains a number of honorifics, which often come in the form of a suffix attached to a person's name. As mentioned above, it can be rude to address someone without using the proper honorific (or the right honorific in the wrong way).

A list of common honorifics:

-san: Probably the most commonly used honorific, it is used as a title of respect among equals of any age, or just for generic politeness. It is often roughly translated as "Mr/Mrs", but it can be used in informal settings as well, and is almost universally attached to names. To a Japanese speaker adding -san to even a friend's name wouldn't necessarily sound stilted.
It can also be used with occupations. For example: kajiya-san (blacksmith-san).
Animals or objects can be addressed as such as well. For example: Tori-san (bird-san). But much like "Mr. Bird" is somewhat childish sounding in English, the same is so for Japanese.

-sama: A large step up in politeness from -san. Often used when addressing one's superiors, and for historical settings the translation of "lord/lady" is fairly apt (modern English, however, doesn't really have a comparable term to denote the level of deference -sama connotes). It can also be used by a business when referring to their customers/clients or when the speaker greatly admires the addressee.
Conversely, it can be used sarcastically to imply extreme disrespect.

-dono: Similar to -sama, and meaning "lord", in the feudal sense. Unlike -sama, however, it does not imply lower status on the part of the speaker. As such, it was a face-saving way for high-ranking people to respectfully address their equally high-ranking peers.
(In modern Japanese the term is considered archaic, and not used very often.)

-kun: Predominately used for male names, as a term of endearment. It can also be used as a generic term for addressing male teens or children, or among male friends.
In business settings it can sometimes be applied to females, often used by older males of senior status when referring to younger female employees. Likewise, a teacher may also use -kun when referring to female students.

-chan: A diminutive suffix, and a general term of endearment, with overtones of cuteness. Most often it is applied to girls, small children (regardless of gender), old people, pets/animals, very close friends, or lovers. When applied to males, its usage can be either condescending or intimate, depending on the context.

More information on honorifics, and a larger list of them, can be found here.