I play a sludgier, noisier, dronier kind of doom metal with a lot of crust punk and hardcore punk influences, death metal influences (mainly Asphyx and other old school ones), so I have an emphasis on stuff like high gain pickups, reverbs, delays, a compressor, a high gain amp. I guess the closest bands to what I am doing in this current project are Black Shape of Nexus, Crowskin, Batillus, Torpor, Thou, Shadow of the Torturer, Whitehorse, etc.
I have friends here who do stoner stuff, in bands like Mammoth, Thirteen Black, Crypt, Hydromedusa, etc. Their sound and set up is generally very different. They seem to like Oranges rather than Peaveys, for example, and use fuzz pedals. Their guitars also seem to be set up more vintage, although Josh from Mammoth does have a Les Paul '70s Tribute with Dirty Fingers pickups.
The guitars I use in the current band are an Epiphone Explorer with a Nailbomb set (alnico bridge) and a Gibson SG Special Worn Yellow with a Warpig set (alnico again), both tuned to C standard. Amp is a Peavey 6534+ with just a clean boost in front and then a heap of pedals in the loop (Custom Comp, Carbon Copy, DD-7, Black Label Chorus, and EQD Ghost Echo would be the main ones, and I sometimes use my PS-6 or my EVH Phase 90). No distortion, overdrive, or fuzz. All the gain comes from the lead channel of the amp and the clean boost, which is only set to 9 o'clock
I have to say that I rarely use the neck pickup except for when I am using an eBow ...