There's a point here that there's multiple definitions for "mod". The kind of mod that basically transforms gameplay to a new game (like the Doom one) is just asking for a new game, even if it is asking for a specific game. This falls in the category of game recommendations.
So what about mods that simply alter gameplay?
The recent Morrowind example you gave boils down to a very vague problem at its core. "I want a better experience". But what defines this? We don't - that's a subjective and argumentative point, that's why we don't cover general questions of "what is the best X". This has been policy even before our game rec policy was in place. This also affects a couple of your other examples, but not all. So let's get to listing mods in general.
Questions shouldn't ask for lists of things, whether it's for a video game or not. We've highlighted all the reasons why these lists are bad in the past - high maintenance that never gets done, poor quality turnout, scale problems, and values dissonance. Let's not get sidetracked on that for now.
Rather, one should try to ask about how to solve a problem or address a concern. As with how this plays out on many other sites, applicable mods and utilities will naturally arrive in the form of answers. These will actually provide conclusion to the question, and that's what helps them become acceptable. Consider how gameplay recording went - the appearance is like a list, but the key component is that it still isn't a list. FRAPS, the top voted answer, concludes the question.
So, in a way, I agree with Oak's middle paragraph - it depends on how concretely defined the problem/concern to be solved/addressed is. And the examples he uses at the end work for me, too. If it's something that can be defined easily (group quests by zone, add a crosshair), then it is acceptable. If it is difficult or subjective to define ("improved" graphics, "add more teamwork"), then it is not really acceptable.