A band member once said of John Lee, in response to John's comment that he could play in a variety of keys, (paraphrasing, here) "sure, John can play in any key, as long as its E" (from Jas Obrecht's book Rollin' and Tumblin', highly recommended). Basically, I have been led to understand that John had a great
preference for E standard. This is what he was doing in the several thing I've seen him do on videos. For example, check out:
http://www.youtube.com/watch?v=rOyj4ciJk34&search=john%20lee%20hookerWatch long enough and you'll see his nearly constant home hand position, which is a two-finger E chord (maybe he covered the 4th and 5th string 2nd fret with his middle finger, but you don't need to - and in fact I think he left the 5th string open a lot). This left his ring finger free for hammers all over the place. I play like this all the time.
Here's another one, a great version of Tupelo:
http://www.youtube.com/watch?v=qThmM5-y_Ok&search=john%20lee%20hookerAgain, watch long enough and you'll see that hand position at around 2:30. Some classic John Lee riffs up close and personal. Unless I'm wrong, it's all E standard.
All that said, in this thread you will see that apparently in his early career he used more open G - I need to check out some of those earlier tunes, since I most know his later stuff which I think is mostly E standard.
http://www.guitarseminars.com/ubb/Forum1/HTML/003008.htmltom