"BrianLe may come on here as well ..."
What's the mythical beast that if you say their name, they'll turn up? :-)
FWIW I'm not a fan of Nalgenes --- heavy, and you have to keep them clean. Like JPete I use soda bottles and/or gatorade bottles, replace them periodically along the way. I think that's pretty common for thru-hikers.
Everyone has a preference for their collection of water vessels. I like a 20 oz or 24 oz soda bottle, plus a 20 oz gatorade bottle, as well as some sort of bladder to make it easier to stay hydrated while walking (I use platypus, but whatever, and switch to bottles only when temps fall well below freezing at night).
I find it handy to use the gatorade bottle for putting drink flavor in (crystal lite or whatever); the wide mouth works easier. I just keep water only in the soda bottle, and use that when needed to help fill the water bladder. Having different bottle types makes it easy to keep them straight.
Water sources on the AT are sometimes a bit of a hump down and then back uphill from the shelter, so it can be handy to have a sizeable bladder or even some sort of water carrier that's comfortable to carry up a steep hill. You sometimes don't want to go down to haul water more than once at such a spot.
On the whole, water is more readily available along the AT than on other trails that I've hiked. That plus more frequent food resupply meant that average pack weight for the AT was relatively low for me, or at least once I got out of the snow (I started in late Feb). This is one area where the AT offers an advantage over the more western trails.
There are a lot of springs along the AT. My hiking partner and I treated water elsewhere, but just drank straight from the many, many springs. For whatever reason (and I really don't know the reason) I got Giardia or something like it in New York. My hiking partner, who treated or didn't treat exactly in the same way did not get it. So who knows. But overall the water sources seemed to me to be pretty frequent and good.
Treatment method: certainly everyone feels that their approach is best, whether chemicals, pump or gravity filter, steripen, or whatever. Aqua Mira drops continue to be my preference. If you're gram counting, then keep in mind that the dry weight of a filter isn't what you should be calculating, but rather the weight of the filter after the first time you've used it on trail and put it away "somewhat dry".
Have a great time! A friend from England is hoping to thru-hike the AT going NOBO with an early start next year, and if so, I hope to join him for the first snowy month or so. My slow motion yo-yo diet plan requires about a month straight of hiking to work off the winter fat! So who knows, it's possible that we'll cross paths.