I like it, i am thinking about doing this at the beginning of next year too.
tissues, either travel packs or full size soft ones since the school kind is probably scratchy.
paper clips,
stickers
rubber stamps and stamp pads,
MEMO PADS, POST IT's you could go to kinkos and they will make up a pad for you that has your kids artwork or your kid's printing of the teachers name on it.
maybe a room deodorizor/spray freshener
Colorful sharpies sharpie permanet markers
Sharp teacher scissors
masking tape, scotch tape, highlighter tape
a Cute Ruler or pointer
Nice Chalk
Change for the vending machine
energy bars or candy bars, gum, mints, snacks, bottled water or the single serve mixes of lemonade
Instant coffee??? or a coffee gift card
Childrens books-- picture books or chapter books, or big colorful photographic coffee table books about what ever they studied with her Like an ocean book or a book about ancient egypt
Of course you wouldn't need to do everything just pick and choose, BUT I'm wondering if it wouldn't be cheaper to do something else. sometimes gift baskets end up being a whole lot more than if you had just picked out one thing.
My guess is that even if she doesn't have to buy her own supplies she would love to have more books in the classroom, and multiple copies are ok. Why not have your son pick out one of his favorite books ( did she read chapter books like Magic Tree House, or Charlie and the chocolate Factory?) and make a book plate and he can write a little thank you and the date and stick it in the front cover. You could even add a little handmade book mark and a gift cert to a book store or a teacher supply store.
If she is as great as you say, she won't really be expecting anything anyway, but how wonderful to thank her specifially for the ways that she has helped your son to grow. HAve Fun!