A cellar may refer to a basement, root cellar, semi-basement, storm cellar, or wine cellar.
In reference to Donnie Darko, "Cellar Door" is a phrase written on a chalkboard that serves as a reference to the idea of phonaesthetics—the beauty of a word's sound divorced from its meaning—and the specific quote by J.R.R. Tolkien who called it the most beautiful phrase in the English language.
Whenever I think of the word cellar, I think of the movie too. Naturally, the process of encrpytion and decryption made me think of putting things in a cellar - a cold dark place suitable for storing sensitive items!