I thought if you say "I don't smoke cigarettes" that would be "[Watashi wa] tabako o suimasen". But I just saw something that said it would be "tabako wa suimasen". Are they interchangable? Is there a difference?
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There are actually three options.
1 and 2, (marking タバコ with the object marker and topic marker, respectively), are semantically the same.
However, 3 (marking タバコ with the contrastive marker, which is also は but has a raised pitch) has the implication that you smoke something else.
So, to answer your question, for a transitive verb, marking the object with を or は both always work (assuming that you aren't constructing an embedded clause), but depending on how は is pronounced, it can potentially have the contrastive meaning.