Series VI - By far the best series.
Series VI was produced quite hurredly by the producers, as the BBC wanted the episodes broadcast much earlier in the year. It's thought that this contributed to the changes in plot, of which there were many. The most important of these, by far, was the removal of the eponymous ship itself; the series now took place on one of the transport vessels, Starbug.
So, what effects did the rush have on the scripts? Well, quite surprisingly, they became much more coherant. For the first time, we had a plotline, and a series arc. It was still as funny as ever, but was also more well-planned and for the first time, took a sense of central continuity. Characters were also given a much deeper level of basic advancement, something absent since Series III.
The witty, fast-paced comedy of this particular series is in many placed preferable to the absurdism of earlier series, and there's an adequate frame to make that humour more structured. It's just a shame that the series had to end on that cliffhanger, leading Rob Grant to leave the series.