I hiked the JMT SOBO in late September/early October (finishing on Whitney Oct. 9th) in '05. It was absolutely awesome - daytime temps in the 60’s and sometimes low 70’s and night temps just below freezing; very few people; NO BUGS; no Rangers; Aspen turning gold; etc. There was a light snowstorm the third week of September (before I started the JMT) which capped all the peaks with a touch of white. The only difficulty was descending the switchbacks on the east side heading down to Whitney Portal - they were covered in ice. That was the only spot where I wished I had my ice-axe with me. (you might consider carrying one)
I talked with every local that I met & all of them said the same thing - your generally good to go weather wise until mid October. An old horse packer that I met in Pate Valley/Grand Canyon of Tuolumne (before I hit the JMT) told me that in the past half century he never saw a major snowstorm (more than a foot) before October 15th.
I have hiked the JMT NOBO in early June in tons of snow and SOBO in the Fall as related above & if I were to do it again I would without a doubt hike it in the Fall again. Even though a heavy snow pack makes the Sierra’s incredibly beautiful, snow travel is tough & the bugs were terrible.
Happy Trails!
freebird