I think there are still some relatively niche use-cases for them left. Specifically, if you're using sufficiently few of them and/or using them in sufficiently rural areas, then all of the polluting outputs other than greenhouse gases become less of an issue, and if you're running them on 100% biofuels, then they can be carbon-neutral. (Also, since vegetable oil doesn't contain sulfur to begin with, an engine running on biodiesel emits zero SOx, which is nice.)
In other words, replacing the cars and trucks that can reasonably be replaced with bicycles, trains, and electric automobiles (ranked from best idea to worst, by the way) is good enough; we don't have to be perfectionist about it.