In the book, Captain Windershins is actually still on the submarine when the Baudelaires arrive. Fiona takes charge and begins to imitate his way of saying "Aye!" after he disappears when they all get back from the grotto. That's also when she changes the motto from "he" to "she who hesitates is lost."
The item on the table that Hook-Handed man examines is called a Sextant and was used to navigate at sea. This particular one has the words "White Star Line: R.M.S Titanic" written on it implying it was recovered from the famous wreck
The quote that Phil says to Sunny is attributed to his Aunt Julia. Seeing as how the quote was said in a particular tone and is about cooking, this is actually a reference to celebrity chef, Julia Child.
Count Olaf talks about developing a new villainous laugh. Act I (2008) begins with Doctor Horrible, also played by Neil Patrick Harris, practicing his evil laugh and remarking, "A lot of guys ignore the laugh, and that's about standards. I mean, if you're gonna get into the Evil League of Evil, you have to have a memorable laugh."