One factor that helps you decide this is whether or not there will be partial shading of the solar array. If wired in series, shade on one part of a panel will affect the entire array, whereas a parallel arrangement would allow the unshaded panel(s) to yield their maximum output.
Another consideration is the voltage of the bank that you're charging. If wiring in series the voltage is additive, which can allow lower voltage panels to charge a battery bank with a higher voltage. It also gives the advantage of allowing a lighter wire gauge. Parallel wiring, by contrast, will yield a lower voltage but will give higher amperage; this requires larger wire, which can add up to significant cost.
What's best on one boat will not necessarily apply to another.