The smoking situation can be a tricky one for roommates. Perhaps you are the smoker and feel that you should be able to smoke inside because you pay half the rent. Or perhaps your roommate is the smoker and their smoking is bothering you. Either way, it's something you should get on the same page about. eHow.com addresses some common roommate etiquette rules such as smoking.
The best thing to do is to just keep smoking outside. Smoking can make allergies worse, and makes all the furniture and even the walls and carpet smell like smoke. These odors are difficult to remove when your lease is up and your landlord may take it out of your security deposit. It also can start a fire if someone falls asleep with a lit cigarette or drops one around flammable objects. The best policy, even if your roommate says they are okay with it, is to smoke outside.
If you and your roommate do decide to allow smoking inside your apartment, make sure it isn't prohibited by your lease and that you are absolutely clear on the rules about it. Also, be careful and always make sure any smoking materials are completely extinguished. Never smoke in bed. Make sure all guests know the rules and follow them as well.
Finally be open to revisiting your policy. If one of you quits smoking, for example, it's highly unlikely they will want to continue to allow smoking inside your home. There's no one one more militantly anti-smoking than someone who's just given it up! If you're the quitter, be kind to your roommate who still smokes and if you're the one who still smokes, be respectful when you request a change of the status quo. You may find that you are no longer compatible as roommates, but still try to be civil with one another until the end of your lease.