Firstly, a few some rules regarding quotation marks:

When a writer puts words inside of quotation marks, he lets the reader know that what he is about to say is a duplication of something that someone else has already written or said. The writer assures the reader that what is in the quotation marks has not been changed at all. Now, as a writer, it's important that one doesn't, change anything at all when quoting; however, using brackets inside of quotation marks lets the reader know that this has been added into the quotation for clarification.

ie: Let's say one would like to quote this: "I am in control." It's all fine and dandy to quote that; however, it may be clearer to the reader if the subject and noun are changed to the third person, as such: Margaret feels that "[she is] in control" of the situation, and .... As opposed to: Margaret feels that "I am in control" of the situation, and.... The latter statement can confuse the reader, for he may assume that the writer meant to refer to himself, the writer, reflexively (see also: Reflexive Pronoun).

Another thing that the writer may add to a quotation is sic. Sic is from Latin, meaning approximately "thus," or "so," and informs the reader that any mistakes within the quotation marks were not his own. ie: "I ain't got any food" is improper. If the writer were to quote that, then he could add [sic] (within the brackets, since this is the writer's commentary) to inform the reader that it wasn't his own mistake: "I ain't got any food [sic]." I, however, believe that if anyone were to assume that mistakes within the quotation marks were the writer's mistakes, that the reader probably would not know what sic means.

Now that that is over, here are some basic rules regarding end punctuation for quotation marks. In American English, the period and the comma always go inside of the quotation marks: "I am a dog." or "I am the man," NEVER EVER do they go outside (unless you're using British English). The semi-colon and colon always go outside of the quotation marks: "These are the ones": or "I am here";
Now, the exlcamation mark and question mark can go inside or outside, depending on the context in which the quotation is used. Here are some basic rules for question marks:
If the writer quotes a question, ie, She said "that one?" Then the question mark, as shown here, is placed inside of the quotation marks. If, however, the writer asks a question, ie, Did she say "this is the one"? Then the question mark goes outside. A problem a writer may run into is when he wants to ask a question while quoting a question: Did she say "am I the one?" In this case, the question mark goes inside of the quotations.

For exclamation marks, the same rules as above can be applied by changing the proper syntax and meaning.