jjnguy's answer captures the part about the history of the meme, but I don't think he captures why it became a meme and what the meme represents.
Basically, the boat-programming question was at the core of what it meant for a question to be programming related. At the time, SO had a lot of questions that were, essentially, "What is as a good such-and-such for programmers?" (e.g. "What is your favourite food, as a programmer?", "What is the best movie for programmers?") After a long debate on the SO blog (since Meta didn't exist at the time) it was eventually decided that all questions like this are not programming related.
The fundamental rule is you can't just stick "for programmers" on a question to make it programming related. The boat-programming question, due to its timing and popularity, is the poster child for this kind of question. Whenever a question is asked today that is not programming related but has "for programmers" tacked on, the boat-programming meme is brought up to indicate this.