Bring a lot of time, a lot of patience, a sense of humor and a lot of money in the form of USD!
All but one of the offices you have to go to are in the main customs building where they will direct you once you leave the ship. Here is what it takes:

Passport and/or Visa:
In order to get your passport stamped you have to pay an entry fee which is $10 per person plus $2 bank charges. We also picked up our visas right here at the border since there is no Turkmen Embassy in Azerbaijan. We paid $51 per person for the visa and $2 each for handling fees. The visas were issued on the spot. (Actually not really: first we had to wait an hour for the Consul to drive out to the port from his residence in Turkmenbashi. His car broke down en route, so we had to arrange for him to be picked up. When he finally did show up and wanted to print out the visas, he noticed that the printer was out of ink, so we had to send a cab into town to pick up a new toner for the printer. Needless to say that this took another hour!)
In any case, check the visa to make sure it covers all the places you want to go!

Customs Check:
At the Customs Office we have to fill out a customs form. They are too lazy to walk out to the bike to check the luggage, so this goes pretty smooth and to our astonishment without additional charges.

Motorcycle Papers:
First we had the official route document filled out. This document is used to calculate the road tax, insurance and various other miscellaneous charges. There is a map of Turkmenistan on it and they mark the exact route you are planning to take. We later have to show this document at every checkpoint. So make sure the route on it is correct and don’t loose it! Based on the route they will calculate the road tax, insurance and other charges you owe.
Once we had this document we visited various officials who put their stamp on it and passed us on to the next post. After the document had all the requisite stamps, we then had to pay said document: We paid $182 for the two of us, so $91 each. The various charges added up to $89 (road tax, insurance, disinfections fee) and of course the $2 bank charge.
Once the fee was paid there was a last stop at the insurance booth, where they filled out an additional document as proof of insurance.
We were then waved back to the customs office where they entered the bike data in a big book. Then they sent us with another document to a different lady who put a stamp on it, no idea what that was. Then we were sent to the police who also entered the motorcycle data in a book, put another stamp on another piece of paper, and with that we were through.
In our hands was no a lot of papers and receipts. The only paper out of that which our will need later on is the travel document which shows your route!

Port Tax:
We got sent to the port authority office, where they filled out a paper. Sent us to a cashier who gave us a different piece of paper and handed us an invoice. With this invoice, we were sent back inside to pay the port tax at the bank window. The port tax was $10.00 per bike plus of course again $2 bank charges. So the charge was $22.00!

For a quick review: it took us 6 hours to clear customs and we ended up paying:
Visa: $53
Entry Fee: $12
Road tax, insurance: $91
Port tax: $12
Total: $ 168 per person and bike

It was pretty straightforward. A young gentlemen who spoke a little English let us know that we had to clear two stations: First we had to go to an office in front of the customs house. There our bike papers were checked.
After that we went into the main building, where we got cleared by customs and then had to get our passports stamped.
Back in front of the building the bikes and passports were checked by two more officers and then we were free to go.
As I said, pretty straight forward, especially if you consider all the work it took coming in. Also exiting the country did not cost a dime. 

Getting the visa:

In 2006 getting a visa for Turkmenistan was a bit of a problem. There are two kinds of visas: Transit Visa and Tourist Visa.

Transit Visa:
You can apply for a Transit visa, which may or may not be granted. It will be granted for three or five days. They decide. We tried to get a Transit visa in Ankara Turkey.
GPS point for Turkmen embassy in Ankara: N39 53.337 E32 52.353
They wanted the following documents:
- 2 filled out application forms
- 2 passport pictures
- 2 copies of passport
- copy of visa for next destination (Uzbekistan or Iran)
- letter for recommendation from our embassy
They said it would take around 15 days to get an answer and they wanted to keep our passports during this time. The reason is that they have to send all the applications to Ashgabat for approval. We did not feel like sitting around Ankara for another two weeks and so looked for another solution.

Tourist Visa:
A ten-day tourist visa might be issued if you book a tour with an agency. This way the agency can arrange for a letter of invitation with which you can then apply for a tourist visa at a Turkmen embassy. This is the way we ended up doing it. We contacted David Berghof at Stantours in Almaty.

Changing money:
As all the fees at the border have to be paid in USD there is no need in getting Turkmenistan currency beforehand. Once in Turkmenistan it is easy to change money on the black market (check at the market or in front of big stores). Don’t change money in the banks for they will of course only give you the official rate, which is only 1/5 of black market value.
On both sides of the border to Uzbekistan you can convert left over Turkmenistan manat or US dollars into Uzbekistan sum. However the ladies on the Turkmenistan side can be very aggressive and are more likely to cheat you than the more laid back male counter parts on the Uzbekistan side.