The Mega Drive/Genesis Lemmings is the better port of all. The ultimate version, the one with the best and most puzzling levels.
Bold statement! Can you elaborate on why you think it's the best of all?
The unique levels it has are of a superb quality. It's a wise decision that some of them replace here and there some of the less interesting levels of Original Lemmings. For example, between Steel Works and Let's Get Together, I obviously prefer the second one. Sega Genesis has not only one unique and full difficulty level, but TWO! Sixty brand new levels, plus the ones scattered along the other four difficulty levels.
Sega Genesis Lemmings has at least 4 of the best and most original levels ever made for the original 8-skill engine: "I Am A.T.", "Lemmings Ark", "Private Room Available", and the two "Fall And No Life" versions. Also, it has "Let's Go Camping", with its childish and unbeliveable backroute, yes, but also with the most elaborated intended solution I've ever seen! And I'm sure I'm missing a lot more to make a point!
Other highlights: "No World Without You", "Anxiety", "Evil Whisper", "The bridge is breaking down"