We went to the Ninja themed restaurant in Kyoto. Its in downtown Kawaramachi so its very accessible. There are usually ninja dressed employees standing in front of the restaurant. You can take pictures with them (we did). We had a buffet dinner, costs 1500 yen for 2 hours. Here is the link - http://ninja-kyoto.co.jp/en/sweets/sweets.php
I usually take visiting friends to Lock-up which is a prison theme izakaya. I've only been to the one in Ikebukuro but I think they also have some in Shibuya and Shinjuku. They have a selection of bizarre drinks and food as well as a prison break every 2-hours or so with actors dressed in costumes. Great fun!
If you are in Tokyo, there is a sumo themed restaurant called "Hananomai". It is right across from the Ryogoku Kokugikan (the Ryogoku Sumo Hall) and close to the Edo-Tokyo Museum. The restaurant has a raised sumo ring right in the center. There are paintings of sumo wrestlers, and everything sumo everywhere. Tables are around the rings and there are a bunch of dining rooms in the back and also towards the front of the restaurant. The restaurant serves izakaya type food; with lots of options to choose from. Food is quite good. There are performances in the sumo ring on Saturdays at 6pm.
I don't know if it is the best but the Detective Café PROGRESS / 探偵カフェ PROGRESS is quite original! There are real detctive who try to explain you about their activities (some speak English) or ask you to resolve problems (trying to find hidden camers,etc). They serve drinks and some strange food as crocodile meat!
Some of the activities are free, some are not. There's also a 1000yen table charge but it's quite fun.
Everyday from 7pm to 4am (irregular closing day)
Saturdays and sundays , it opens as a café from 11:30am to 5:30pm
Détective Café PROGRESS / 探偵カフェ PROGRESS
Adress : 9th floor, Kizuna Building II 2-47-12 Ikebukuro, Toshima-ku, Tokyo
Tel : 03-6698-2263
Access : Ikebukuro station, North exit