In addition to responding to each allegation in a complaint, an answer might also, and usually does, include affirmative defenses.  You might think of an affirmative defense as an objection to the plaintiff’s claims that might not otherwise be obvious from reading the complaint and the rest of the answer. The idea of including an objection as an affirmative defense in the answer is to prevent the plaintiff from later claiming surprise when the objection later comes out during the course of litigation, particularly trial.

There is no set list of affirmative defenses. Theoretically, you could have an affirmative defense that is unique to the facts of just one case. However, there are certain affirmative defenses which are fairly common, such as: failure to state a claim for which relief may be granted, lack of subject matter jurisdiction, lack of personal jurisdiction, failure to exhaust administrative remedies, improper service, lack of standing, and failure to comply with the statute of limitations.

For a little more about certain statutes of limitations, see the article dealing with a motion to dismiss..