I don't know I'd say best theming, but one of the best overall gift shops in WDW is Mitukoshi.
The very best themed gift shop(s), IMO, are the pop-up tribute gift shops at Universal. If you have not been before, Universal does pop-up gift shops that only last a few months. They are part gift shop, and often part walk-through attraction. They had one themed to Jurassic Park that was really fun. It had some merch, but also photo-ops with dinosaurs. They currently have a great gift shop themed to Wicked that has costumes from the movie. It is worth walking through just to the shop, costumes, and movie props.
I don't usually buy stuff, but for theming: UK shops have nice theming, in AK the Pandora gift shop has good theming. I haven't been there in some time, but the gift shop at Animal Kingdom Lodge used to have great themed merchandise. The last time I visited it was more generic though. The Winnie the Pooh and Memento Mori gift shops are well-themed. Take a moment to check out the wall decor in MM, some of the images shift/change. There aren't any shops I really love right now in HS, but prob the Star Wars ones are among the best themed. The one at the end of ToT used to have some fun theming, but last time I visited the merchandise was fairly generic. The GoG one is fairly well-themed.
Right now is the Art Festival at Epcot, a lot of unique art and merchandise for the festival.
Overall, I gotta say the merchandise over at Universal has considerably improved in the last few years. They have many well-themed gift shops. One of the best is Olivander's. Other fun ones are the Minions, almost any other Harry Potter one (Honeyduke's, Weasley's, the rope shop with the talking mirror), and the Marvel ones come to mind. I had a chance to visit the new Stella Nova hotel, and they have a few items for Epic that - I think- are unique. They have more/wider selection of Epic merchandise at the preview Center in Citywalk than at Stella nova, but I think several SN items are unique to that shop. I got a really fun spirit jersey style shirt themed to Dark Universe there.