I would add that most industries that deal with metals and chemicals (ex steel mills and refineries) are pretty noxious, but otherwise they're mostly alright.
There's a sugar refinery in Toronto that's right next to an urban beach and media headquarter, and has a large condo project under construction on the other side.
You can take in the sweet smell from the beach while watching the big ships unload their cargo.
There's a few sites of contention in Toronto though. There's a new lakefront condo community growing in a former suburb West of downtown and most of the remaining land is currently being developed, leaving only a large Mr Christie cookie factory. There's also a Cadbury factory that's opposed to the rezoning of some nearby industrial land to allow residential development since they're worried the new residents will complain about their industrial activities. The Port Lands are a huge industrial area that's set to be redeveloped, although there isn't a whole lot of industry there now. If there was more substantial industry I would be opposed to the redevelopment of the area. There's also a large meat packing (slaughterhouse too?) plant very close to downtown with a lot of new condo development nearby... that's one case where I don't think the industrial activity is well suited for the area.
Generally though, I think industrial uses have a place in cities. They don't make use of the land as well (generally) as midrises/highrises, so they might not make sense right downtown, but I think it would be good if the less noxious industries would be located in walkable areas, especially next to harbours and railways.