I just got back from a vacation in Japan and visited the following cigar lounges in Tokyo:
Le Connaisseur in Shibuya: roomy cigar lounge behind Shibuya station with a decent selection of standard marcas and vitolas. However, not too many regional or limited editions (only RA Club Allones, R&J Capuletos, Monte Dantes, La Gloria Cubana Revolution). I smoked a Monte Dantes (price was around 6000 yen) and thought it was okay but very spongy—I think the cigars there are over humidified.
Torcedor near Maihama station: another roomy cigar lounge, but the selection is very limited. No regionals or limited editions. All cigars are wrapped in cellophane (weird). Half the cigars were NC. I smoked an Epi 2 and Siglo I and paired them with an Old Fashioned and glass of Longrow scotch. Total damage was around 8500 yen.
Cigar Club in Azabudai, near Tokyo Tower: very small cigar lounge (mostly bar stools), but it had a wide selection of LEs and REs. Very knowledgeable and friendly staff that can speak good English and will show you aged stock if you ask (e.g., Bolivar Libertador with a 2013 box code). The only place I went to that carried Talisman (over 10000 yen a stick). I picked up a couple of sticks to sample back home.
Prices are pretty uniform in Tokyo and cigars are expensive.
I flew out of Haneda airport, which unfortunately didn’t carry any CC at the duty free shops, just Alfred Dunhill.