While this is a somewhat old topic, it looks like we could use a little traffic and this topic interests me:
I don't use a neck pickup too often, but when i do it's for bluesier stuff ala Allman Bros. That creamy fat tone. Not muddy.
All the Brothers (Duane, Dickey, Warren, DDT, Derek, Jack, Jimmy...) used the neck pickup a fair bit for both leads and chords. Neck pickup use is a big part of the ABB sound. In most cases they are using a stock, and covered, PAF, in both positions.
Even when Dickey uses a strat, which he does quite a bit, he uses the neck position with an unknown (to me) rail pickup there. Jack Pearson also used rail pickups in his strats, although he often used the bridge position much more than the others.
It is reported that Dickey's rig can sound harsh and bright in the hands of others but as soon its in Dickey's hands the tone is warm and creamy. Another case of "tone is in the hands". To get closer to that creamy sound at less than arena volume, many of us could probably use a slightly stronger neck pickup, such as the Breed neck, or the PAF Pro.
Duane found a set of PAFs in one of his gold tops that he transferred to other guitars when he found a new number one. These probably had a bit more output needed for slide work. It is said that he wasn't 100% happy with any guitar until he found a tobacco burst les paul in the last months of his life.