Openstreetmap

In the past I would use Ferrylines (see below), but this website has been down for a while now, promising to come back online soon. Until that happens, I use Openstreetmap:

• Browse to Openstreetmap Turbo to search for ferry routes
• Navigate the map to the area of interest
• Click "Run"
• When warned for "Large amounts of data", click "Run anyway"

The result might look something like this:

Openstreetmap rendering of ferry routes.

It does not discriminate between overnight ferries and short ferries, but typically, longer routes run overnight and shorter routes run during the day. You can check out details by clicking on a route. With some luck, there is enough information there such that you can use a web search engine to get additional details.

As per this comment by asdfex, the difference between blue and violet lines is not relevant (route represented as a single way or a collection of ways).

Like with other web sources, information may be out of date or incomplete. On the plus side, when information is out of date or incomplete, you could go and edit Openstreetmap yourself to remove or complement it.

It should be possible to run more advanced queries and select ferries based on particular characteristics (as long as those characteristics are included in the Openstreetmap database). This is technical and works via the Overpass API query language. Related questions can be asked at the GIS Stack Exchange.

Ferrylines

Update March 2023: The ferrylines.com website is currently down, apparently for maintenance, but is supposed to come back "in short time".

Original answer from 2017

In my experience, the most up-to-date source for ferries in Europe and in fact around the world is ferrylines.com. They have a reasonable good interface.

Although you cannot specifically search for overnight ferries, a good hint for “overnight’ is that the crossing lasts at least 6–8 hours and that it operates at most 1–2 times per day. Also, (almost?) all overnight ferries are primarily ferries for cars and trucks, but do also permit passengers (some roll-on roll-of (RORO) ferries accept only trucks, but you’ll find those mostly on freight ferry websites). Even the Cunard Line passenger liner from Southampton (or Hamburg) to New York is listed, as are, for some reason I don’t quite understand, Eurostar trains.

Snapshot from Ferrylines.com. My apologies for the low resolution image; I could not get it under 2 MiB otherwise.

DFDS Seaways operate overnight ferries between Copenhagen and Oslo.

Ferry from Helsinki, Finland to St. Petersburg, Russia where you get 72 hour visa-free access to Russia via the St. Peter Line. I spent ~50 euros one way where I got a 4 bed windowless cabin. We departed around dinner time in Finland and arrived in Russia the following morning. The ferry has bars, restaurants, sauna/pool, and shows. A great way to begin a trip to Russia especially if you don’t want to deal with the onerous visa process.

I have to mention the Norwegian “Hurtigrute”, which runs between Bergen, Trondheim and even further up north (it stops at a lot of places in between).

There’s also a overnight ferry route between Tallinn and Stockholm.

Not exactly between cities, but there is an overnight ferry in Scotland, sailing from Aberdeen to Lerwick, in Shetland. This is operated by NorthLink Ferries, and takes about 12 hours, or 14 hours if it is going via Kirkwall in Orkney. You can book a cabin, or cheaper just to sleep in a reclining chair.

The night ferry Harwich/Hook of Holland (Hoek van Holland) is a great way to get to/from the UK. The ferry is really comfortable and good value. The only downside is that you can’t quite get a full night of sleep – more like 7 hours maximum (realistically more like six). It is not too hard to get to Harwich from London and you can get anywhere in the Netherlands from Hoek van Holland; it is a small country with an efficient railway network and English is widely spoken.

The ferry is mostly used by truckers and people with cars, but I have had no problem using it as a pedestrian. I’ve done it twice.

There is a night train between Copenhagen (actually, Malmö) and Berlin, arriving between 6 and 8 am. The whole train gets inside a ferry to cross the water, and you can freely go to deck. Booking well in advance, the tickets are cheap.

One other option which accomplishes the goal of traveling by night while sleeping and arriving at your destination well rested is City Night Line by Deutsche Bahn and their European partners.
http://www.citynightline.de/citynightline/view/en/info/infomaterial_en.shtml
For example, there is a daily connection starting 8pm from Berlin/10pm from Hanover and arriving 9am in Paris.

Condor Ferries run Jersey (St Helier) to Portsmouth departing 21:10, duration 9h 20m (about £30 per head, single).

DavidB has perhaps the most comprehensive answer (= the Google Answer)… but here’s some bits that we’ve done over the years.

If you are in the Med, there are a lot that go to/from Marseille as well as Barcelona. Obviously Corsica/Sardinia/Sicily are paired up there. There are a lot of different operators (Corsica Ferries, for example); start looking in Marseille and then take it from there.

I’ve done the Stockholm-Åland-Turku journey on VikingLines before and it’s quite convenient, especially since you can choose to have a few days stopover in Åland without any additional charge (usually).

Some of the overnight ferries get (in my opinion) stupidly expensive. The Rostock-Helsinki ferry, for example, really makes one do the fuel cost comparison for driving via Sweden or the Baltics… There’s more competition over the English Channel, so the Hoek van Holland-Harwich ferries always have some kind of deal going on.

One popular overnight ferry close to where I live is a DFDS ferry from Newcastle to IJmuiden (Amsterdam).

Both cities have plenty to offer for short trips and the fare is quite cheap if you get an off season deal and are a foot passenger travelling in a group.

Last time I got it, it took around 14 hours overnight.

Alternatively here is a map of some of the major European ferries. Simply Google the route and you will find the operator. Unfortunately, there wont be many overnight ferries because of the short distances between land.

There are some ferries between the Scandinavian countries and Germany, e.g. Oslo-Frederikshavn, Oslo-Kiel (takes more than a night), Gothenburg-Kiel and Trelleborg-Rostock (don’t know how long this one takes). There was a ferry from Esbjerg (DK) to Harwich (UK), but it shut down.