Before the modern ballot came to the United States, most places required people to vote the "party ticket." You were literally handed a pre-filled out ballot with the candidates names pre-selected. Later, we started giving people choice to vote for candidates from different parties and even write in others.

Generally, it's very difficult for a write in candidate to achieve success, but it used to be much more common, especially in state primaries running for the presidential nomination. Hoover, Roosevelt, Eisenhower, Nixon, and Kennedy all won some presidential primaries on the strength of write in votes. It wasn't exactly ubiquitous, but you could fail to get your name on a ballot and still win a primary if you had the name recognition and political backing. One of Ralph Nader's recent campaigns garnered several thousand votes in the New Hampshire primary. To answer your question directly, however, I don't think there has ever really been a sustained write in campaign large enough in US Presidential elections to make a huge dent. 3rd parties, yes. But write in candidates? No.

After reading your question I became curious how many people write in nonsense candidates every four years. Apparently quite a few. One newspaper in Georgia reported receiving at least 2,000 write in votes, some of them for Mickey Mouse and Elvis. Others vote for candidates who lost in the primary or are simply confused as to how to fill out the ballot.

Here's an interesting possible answer: Abraham Lincoln. He was left off the ballots of all the southern states in 1860 and won anyways. I could imagine places like Missouri, the Shenandoah Valley and western Appalachian mountains running into trouble attempting to vote for Lincoln. Does anyone know if this happened (should be easy to find out since i'm guessing if this happened there would have been some election violence)?