Warnemunde is a 5 minute walk from the port . We have been to Berlin before so we opted to take an independent tour of Warnemunde and Rostock. Upon exciting the ship, there will be directions on how to get to Rostock. It will tell you which train to take and where. However, for us, as we walked to the town of Warnemunde, along the harbor, there is a ferry that will bring you to Rostock. It runs every hour. The ferry between Warnemunde and Rostock takes about 30 min. The ferry cost 12 Euros roundtrip. The tours from the ship is a ripp-off. We took the 1045am ferry trip, then toured Rostock and had lunch there. You can get a map from one of the info offices as you walked towards Rostock, the town is very easy to tour as it is very small. We then took the ferry back to Warnemunde at 215pm. The last trip is 315pm to Warnemunde. Since the ship does not leave until 11pm, we had enough time to wander around the pretty town of Warnemunde, they have shops, restaurants and watch the uniformed street singers by the bridge.
One of my favorite ports is Tallin. Again, there is no need to take an organized tour. It is also a walking distance from the port about 15 minutes, but if you dont want to walk and start your tour from the upper town of Tallin, you may take the Taxi just after you exit the ship. There will be taxis waiting outside. Just tell the taxi driver to drive you to the upper town, it cost 15 Euros. That is what we did and the taxi driver gave us a map of the town, he told us how to start our tour from the upper town and then how to get to the lower town. It is very easy since tallin is also a very small town. It was so cold in Tallin when we got there so I ended up buying Tallin wool products. We had enough time to walk around the walled city, shop and lunch at the square. This is a nice town to just tour it in your own rather than being hurried. You want to take time and walk the cobbled stone streets and just wander around. If you take the organized tour, you will be rushed. After spending enough time in the walled city of Tallin, you may walk back to the ship or take the taxi.
Except for the weather at that time we were there (rainy and cold), St. Petersburg is a wonderful city to explore, there is a lot of history and places to see here. This is the only port where we have to hire a tour guide. I did a lot of research before deciding which tour and which tour agency to take. Based on my research comparing the tours provided by the cruise ship and the private tour agencies in SPB, you will get more in terms of time and less people when you book with a private tour agency in SPB. When you book with the cruise ship, there will be 50 of you in a bus, but with the outside agency, you can choose how many are you in the tour group. You only have 2 days in SPB and there is a lot to see, so you have to maximize the time. There are so many private tour agencies in SPB, you can find them mentioned here in this site, but I chose SPB-tours of Viktoria. We had a wonderful tour guide and I was very satisfied with the service. I am sure the other tour agencies are good too and I recommend others to do their research.
I also recommend attending an art lecture about the hermitage if you plan to tour the hermitage museum, it will enhance your experience if you know the artists and the arts you expect to see. The ship has an art lecturer/dealer on board. Look for schedule of lectures on the ship's newsletter.
Again, there is no need to take the ship's organized tour. Helsinki can be done on your own time and pace. We took a hop on hop off bus to Helsinki. When you exit the ship, you walk few minutes and the HOHO bus will be waiting outside for passengers. The HOHO cost 25 Euros. They accept credit cards. It is a good way to explore the city on your own. The first stop will be the flea market - I bought a beautiful necklace there for just 8 Euros. But if you are not into second hand stuff, don't get off here instead proceed to the next hop off.
Do not even bother asking the tour desk staff about the existence of the HOHO because they don't know. Either they intentionally won't tell you or they simply just don't know. I know because I asked where to get to HOHO and I was told there is no such HOHO, but when we exited the ship, the HOHO was right there.
The ship's newsletter will tell you about the complicated way how on how to get to Stockholm, first by bus, then by train. But again, Stockholm can be done on your own time and pace. There is a tender for this port, after you get off, there will be a lot of buses waiting. Look for the bus that has a sign Hop on Hop off. Prepare to pay cash, they accept Euros and dollars, but won't accept credit cards. Before we went on the cruise, we studied first which places to go see so we can maximize our time. Search the Stockholm open top tours and see the different stops and decide which stops you are going to do when you get there. It is the best way to plan out your trip before you get there so you will have a more enhanced experience. I recommend stopping at the Vasa museum, Gamla Stan, if you have time, the Nobel Museum is at the Gamla Stan square near Stockholm Cathedral and Royal Palace. If you also want to visit the Ice bar, there will be a long line to get in so time accordingly.
Again, do not bother asking the tour desk about the existence of the HOHO because they are not aware of its existence. I know because I asked and I was told there is no such HOHO.