6:02 p.m. on March 2, 2006 (EST)
Direction on the JMT depends on a number of factors. If you go in early season, going south to north means you are following the melting snow and have a better chance of not having as much problem going over passes. North to south means encountering some of the highest passes with a lot of snow on them.
Late in the season, south to north runs the chance of hitting snowstorms by the time you get to the northern end. Too late and Tuolumne is closed, and you have to slog through snow back to the Valley.
Most people I know have done north to south. Part of the thought is that by the time you get to Florence Lake (actually a few miles east of the lake), you are in better shape, boots well broken in, and the heavier load the first couple of days is easier to handle than having the heaviest load right from the start.
Another consideration is that north to south, you can camp a couple days in Tuolumne to acclimatize a bit (8600 ft), then you get a short 2 days from the Valley with a light load to start getting accustomed to the pack (happens with everyone, including "hardened" hikers), and you have a good shop there in Tuolumne to do any needed adjustments. The next day up Lyell Canyon is fairly gentle climb. Going south to north (best choice in a heavy snow year) means you have a steep climb right at the start from Whitney Portal (8200) to the pass (13,700). You might not be able to camp at the Portal the first couple of nights (small campground), so acclimatization is much more of an issue. And if you suffer from AMS on that first day or so over the pass, you have no retreat except over the pass (Trail Crest), putting you back at altitude, which will just exacerbate the AMS (or worse).
At any time, you are right that there is a big gap for resupply between Whitney Portal and Florence Lake (Muir Trail Ranch, which is actually Blaney Meadow), over 100 miles or almost half the trail. Going either way, you have 5-10 days of food to carry. Some people go on short rations for this section - lightens the load, but puts you way behind the energy replenishment curve. It is probably easier for most people to go short rations at the end of the trip than the first part.
If at all possible, try to have a friend bring in re-supply over Kearsarge. This will cur the smount you have to carry from Muir Trail Ranch. You will have to coordinate meeting time, since there is no food drop. If you don't meet up for some reason (miscommunication, some access problem, some delay on your part), you will be forced onto short rations. This coordination is easier on a south to north itinerary, since you are in cell phone coverage in Lone Pine (below Whitney Portal) just a few days before the meeting. Communication from Muir Trail Ranch is problematic, so coordination is harder on a north to south itinerary. Well, you could always use sat-phone, but then that takes away from the wilderness experience.
Another consideration is access to the start. Commercial transport to Yosemite Valley is pretty straightforward. Plus there is a bus between the Valley and Tuolumne, so you don't need to deal with a car. There are a couple shuttle services along the eastern Sierra, so pickup at Whitney Portal and dropoff in the Valley is straightforward (but costly). Going the other way, commercial access to Lone Pine is a bit questionable these days, with the changes with Greyhound.
I know a few people who have done it both directions. They almost all thought the north to south worked better.