"Bellini", the night train from Rome (Termini) to Siracusa, leaves around 9pm, and is loaded onto the ferry across the Straits of Messina very early the next morning (6-ish). You just lie in bed while it's loading, and can then go up and have a coffee on deck and watch the light over the coast of Sicily, although you could just stay in bed and wait for the attendant to bring you the cappuccino or espresso you ordered the night before (at the carriage door, when you get on).
There are four-person couchettes, but there's something really romantic about proper sleepers, and a two person compartment (single bunks with proper sheets, plus complementary toiletries, mineral water, coffee...) - costs just €75 pp. If you want something more luxurious you can have a double bed compartment with ensuite shower etc for €140 pp.
The air conditioned train then follows the coast, through Taormina, and arrives in Siracusa at about 10 am. We love going to bed and waking up 500 miles away, right where we want to be - it's a great way to unwind at the start of a holiday.
Italian night trains are all good value, but the crossing - and the destination - makes this one the best.