The shops that I seem to always find really cute or interesting things in (whether I bought them or not) are:
China Closet on Main Street in DL
Disneyana on Main Street
Disneyland Gallery on Main Street
Fortuosity on Main Street
Market House on Main Street
Pieces of Eight in NOS
Le Bat en Rouge in NOS
Gag Factory (in ToonTown)
Off the Page in DCA
Engine Ears in DCA
Fantasia shop in the DLH
The Emporium on Main Street and World of Disney are good shops for lots and lots of things, as is the Star Traders or whatever it's called in Tomorrowland, but those are all larger and more obvious choices. In fact, I think a lot of people heard straight to the Emporium and they skip Disneyana or the China Closet, which are little gems.
World of Disney is enormous - so if you go in there with your whole group, make sure to keep an eye on everyone because it's easy to lose people in that store! Or if you split up, arrange a place to meet up again. I lost a friend inside that store, simply because one of us turned to look at one thing and the other one walked a few steps and suddenly we couldn't find each other!

It's a huge store.
Downtown Disney has shops like Anne Geddes, Sephora and Basin. Basin sometimes sells little Mickey-shaped soaps or other Disney products. And, of course, there is Build-a-Bear, which is great for kids. Rainforest Cafe actually has a little shop with some really cute things as well.