smoking yaoi

http://www.mangago.me/read-manga/yuki_no_shita_no_qualia/ here's one (it's shounen ai though)

Errrr I'm trying to remember... ok if I find some others I'll tell you but for now I have only 2 (dammit why didn't I tag that)
Saezuru Tori wa Habatakanai
Yondaime Ooyamato Tatsuyuki (and there's a smokey kiss at the end gosh I'm going to read it again)

http://www.mangago.me/read-manga/1_2_cigarette/

http://www.mangago.me/read-manga/smoker/

http://www.mangago.me/read-manga/by_my_side/
plus a tag I made cos I loves these stories:
http://www.mangago.me/people/tag/179149/Smoking+Room+%E2%9B%BD/

Oh all suggested above are great manga.