*2016 update: see link here.
My top pick: Cafe Nine9 Style, Hongdae
Nine9 are a small company that sell clothing and accessories for ball jointed dolls online, and they have also opened a physical outlet and cafe. I really like this place because they have a little 'photo studio' corner set up, where you are free to use their sets, props and lighting to take pictures of your doll. The cafe has a great atmosphere, and there is a good selection of things to buy in the store area.
Cafe Nine9 is located on the 'other', quieter side of Hongdae station. Come out of exit 1, walk 140m and take a right at the large junction. Walk 340m and take a left just before Shinhan bank. The cafe is on the corner of the next street, on the 3rd floor.
Cute and quirky: Alice's Teapot, Buam-dong
If you're not into ball joint dolls, there is a cafe that will appeal to collectors of other kinds of dolls, and even to those who aren't doll lovers, too. Alice's Teapot is chock-full of vintage fashion dolls and children's dolls, as well as old English style tea sets, creating an 'Alice's tea party' vibe. They do a great cup of tea, served of course in one of those beautiful cups, and I think they also serve cakes and desserts. There are soooo many dolls everywhere in this cafe!
Alice's Teapot is in the lovely neighborhood of Buam-dong, pretty far from any subway stations. I discovered it accidentally when taking a long stroll around the area. It's very close to 자하문터널입구 bus stop. Address: 종로구 부암동 208-39.