There's a couple of Spectre Sound Studio videos where Glenn demonstrates the total lack of difference in guitar pickups, while making absolutely and completely clear that he's talking about heavily distorted guitars playing metal. And yet he still gets people complaining that the pickups sound different when played without distortion, which wasn't his point.
Low End Lobster does a few comparisons between different ranges of bass with different pickups, eg the Ibanez EHB series with Bart BH2s on the low end ones and Nordstrands on the top of the range (although there's now another range with Fishman pickups), and also the same basses after he's changed the pickups. Pickups will colour the sound to a greater or lesser extent - I would say that the ideal is a pickup that doesn't significantly colour the sound, so you can add colour of your own. That means it's got to put out a full range of sound pretty evenly, not be weak at the bottom or top end, because you can always take away but you can't add what isn't there. Alternatively, you get a pickup which is pre-coloured the way you want it, though that then limits the range of sounds you can get from it.