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Series vs Parallel Wiring on Bass Pickups

Depends on the specific pickup(s) and the sound you are after.

In general series is louder, more mid heavy. Parallel is quieter, clearer, more mid scooped. This assumes the same pickup and choosing between the two. A pickup has its own voice and can influence which wiring you may prefer.

I like both and like being able to switch between them (even though most of my basses do not have a series/parallel switch).
 
I can't speak to when one would work better than the other, as this is largely subjective, but I recently did a comparison of series vs. parallel wiring using the G&L MFD Split Coil pickup in my Squier medium scale P Bass. Here's the link to the thread with the comparison video including sound samples and frequency response plots.

In short, I found the parallel wiring to reduce the level by about 5 to 6 dB while retaining significantly more high end. I didn't find the parallel wiring to be mid-scooped at all with my setup, in fact the frequency response was nearly identical up to the point where the series configuration began to roll off the high end. For my use I prefer the broader frequency response of the parallel wiring and I don't mind the loss of output as I can easily compensate with a little more amp gain, and then use the amp's eq to tailor the tone.