On the advice of friends and acquaintences in the marine diesel manufacturing industry, we have always used two additives in our fuel. One is Biobor JF from Hammonds, which is a bug killer. THe other was a Hammonds lubricity additive which they have since replaced with a newer product called Lubribor, which is what we use today.
The subject of fuel additives is always a good way to start a hot debate, but we decided to follow the reccommendations from people in the diesel engine business and leave it at that.
We have no idea if the additives are actually doing anything. But after 16 years of running this boat the 41-year-old engines don't smoke any more at startup than they did when we bought the boat, they don't smoke at all after startup, and the fuel filters still look as clean when they come out as they did when they went in other than being dyed red from the fuel.
Our fuel system (installed by the previous owner to replace the original system) is gravity-operated: all tanks feed from their lowest points so nothing remains in a tank when it's empty. The only pumps in the system are the mechanical lift pumps on the engines.
I have never seen any water in the filter bowls even though our fuel management process has one or the other pairs of saddle tanks empty almost all the time unless we are going on a longer cruise. (We alternate the empty tanks because they're stainless, which is a whole other subject.)
I know condensation can happen because we always got water out of the tank drains before the first flight of the day in the airplanes I flew in Hawaii, even though the tanks had been drained of water the day before. But for whatever reason, condenation does not seem to be an issue here. No boaters we know have every mentioned encountering it, and none of these boaters keep their fuel tanks full, even when they are not going to be using their boats for awhile.