personally i'd say little john 0.21 at the moment (and mainly because i have saved a billion "save states" with it)
for me it works pretty much perfectly already with all the games i've tried so i'm not sure how it or any of the others are going to get any better than this
I don't think there is much in it between NesterGP and LittleJohn. However, the only NES game I actually want to seriously put any time into is Elite and that only works on LittleJohn at the moment.