Some general tips:
Visit hiker boxes before you go to the store to shop for supplies.
Carry the gear to camp comfortably. A few extra ounces for an inflatable pad and enclosed tent will make it much easier to skip a night at a motel.
Seek out AYCE buffets.
Split the cost of motels with other thru-hikers.
Get cash back at store counters rather than racking up ATM fees.
Shop at grocery stores rather than convenience stores when possible, even if it means a longer hitch.
Plan your town visits to head in in the morning and head out in the evening if possible. Skipping the evening in town and the associated motel costs is the easiest way to economize.
Take your zero days on the trail rather than in town when you can. Its very possible to do laundry, wash up, and so on on the trail. You can carry heavy food out of town with you for that first day off on the trail.
Do your research and learn the places that are expensive to shop for food (eg Kennedy Meadows, Vermillion Valley), mail yourself packages from previous stops to these places.
Finally – don't go too nuts on economizing. A thru-hike is a once-in-a-lifetime experience, give yourself enough cushion that you can do it comfortably. Unlike a "real-world" purchase, like say buying a car, where the difference between $13K and $14K isn't really much of a difference at all, a thru-hike is one area where an extra $500-1000 can make a giant impact on the experience. There are people on the AT and PCT every year who have to drop off because they tried to cut things too close and ended up running out of money, and to me this would be devastating. Don't be one of these people.