Excursion rule of thumb: (in most cases) the further your tour destination from the ship, the better off you are booking a shore excursion as opposed to venturing off on your own.
We rarely book shore excursions, preferring to see ports of call on our own. However, when traveling, there are lots of variables over which you have no control. This is not usually a problem in most places, but having just returned from a Baltic cruise, I'd think twice about getting from Rostock (Warnemunde) on your own. Remember, the ship will always wait for passengers delayed on ship sponsored shore excursions; it won't wait for you if your watch stopped, your train is delayed, or there's a sudden wildcat transportation strike (quite common in Europe).