Crossing Caspian Sea from Aktau to Baku (by motor bicycle) my experience July 2013
First I have to say, you need a lot of patience. If you are in hurry, don’t go! But if you have a lot of time, the crossing is a beautiful experience.

Schedule
There is no fix schedule. If a vessel is full then it leaves the port. In my time there was a ferry every week. I heard from other travelers that they had to wait two weeks or they have left the port in Baku and spent 3 days a few kilometers off the port of Baku, because there were no landing stage in Aktau was free. Also, because of bad weather, there may be a delay of several days. Note that you have enough time before the visa expires.
On which day the ferry leaves no one could tell me. So I was traveling to the port every morning to be sure I don’t miss the ferry. The Ticket Office calls you (or the hotel) to say that, today or tomorrow the boarding begins.

Registry and tickets
In order to get a place on the boat you have to register at the port.
Coordinates: 43.603394, 51.220742
The registration costs 4550 tenge (~ 30 USD, as of July 2013)
Then, you need to buy a passenger ticket.
Coordinates: 43.640881, 51.170971
The ticket costs 18300 tenge (~ USD 120 was in July 2013)
The cost of the transport vehicle to be paid in Baku (see below).

Boarding
The boarding begins at the same point as the registry is. Then you have to go from one office to the other. These are scattered throughout the port and you have to ask sometime for the exact locations. The people are helpful and nice. Likewise, the customs, because I had an incorrect Custom Declaration and the officer has helped me tremendously to solve the problems and he didn’t ask for money! You have to pay on the ferry nothing further addition to the costs for food, administration, passenger ticket and vehicle transportation.
The whole boarding took all day long. First they load other goods and then trucks (first in last out). Time for everything: about 8 hours (including waiting time).

Ferry
On the ferry there are several cabins. I stayed with 3 other travelers in a 6 bed cabin. This was dirty and does not smell good. You can buy some food on the ferry. This is relatively expensive (a delicious soup with some meat and bread, 5 USD).
The ride on the Caspian Sea was at night and I was in Baku in the early morning. Journey time: about 30 hours.

Unload
The immigration process was on the ferry. Then unload was quickly and I had to wait for 3 hours because the custom officer has worked at night and now wants to sleep. Then again wait an hour, because of a computer problem. Depending on the port in which you arrive, you have to drive to another place in Baku to complete the customs formalities. Here you will but accompanied and an custom officer shows the way.
The cost of the vehicle must be paid in Baku. It is charged according to the length of the vehicle and the length was measured on site. For my bike one meter has been charged, which is very generous, as the bike is almost 2 meter long. The meter cost me 90 USD (as of July 2013).

As I said, you need a lot of patience, but if you have then it is an unforgettable experience. Enjoy it.