If you can swing it, designate a spot in the staff parking lot for your room mom. Put up a sign with her name, or "Volunteer of the Year." This is a fabulous, thoughtful gift for anyone who spends a lot of time at the school, and has the advantage of costing you nothing.
Give her a gift that encourages her to take a few minutes a day for herself. She might like a gift card for a local coffee shop, her favorite author's newest book and a box of chocolates or a pair of tickets to the theater or symphony. A day pass to a local spa would be a wonderfully luxurious gift.
Bouquets of fresh flowers may seem cliché but they are a wonderful way to express your thanks for a job well done. If you know that the mom in question has a green thumb, then a vigorous house plant or a flat of flower or vegetable starts for her garden would also be a welcome gift in the spring; give her a large poinsettia or a flowering "Christmas" cactus as a winter floral gift.
A photo of the smiling students she's been helping all year are a great present for a room mom, and there are many ways to make the presentation. Give her a copy of the class picture--or take one yourself with a digital camera and have a 4-inch by 6-inch print made at a photo shop--and put it in a silver frame with "Thank you!" engraved on it. You can also have photos printed on t-shirts, coffee mugs or mouse pads for a very personalized gift.
Room mothers always have a lot to carry, so buy a large, plain canvas tote bag at a crafts store. Use fabric paint to write, "Thanks For the Helping Hand!" on the bag, then have the kids decorate it with their hand prints; use different colors of paint for the hand prints.