Well, the way I've tried to set up the newb documentation flow is basically this. Hopefully people will stumble upon the About page first and then go something like:
About ->
Download and Installation ->
Tutorials or either the fortress or adventurer quickstart guide -> reference overviews -> rest of wiki
The about page mentions graphics sets but only as a sort of "response" in mentioning that some people find the ascii ui troublesome. (Perhaps the link to the graphics sets page here should be removed from the About page, but it seems worth at least mentioning at that point that there's a solution to that particular issue some people have with the game.)
Right now, Download and Installation links to graphics packs, lazy newb pack, and dwarf therapist but doesn't really recommend anything. The reason I thought it made sense to mention these things in a clearly marked third-party package section is that some people are immediately put-off by the "ascii" graphics and may not even want to start without a graphics set, so it seems like it makes sense to know about those options ASAP. Also, many people have complained that it took them too long to even hear of DTs existence. I would have wanted to know about LNP earlier but I had to really poke around to find the utilities page, LNP, or any utilities really.
Graphics sets and LNP aren't mentioned in any "quickstart" guides or tutorials. Only DT is, and then it's only mentioned in the sections on managing labors as an option that it might make the UI much easier for most people. This is when I would have wanted to learn of it.
Anything other than graphics sets, LNP, or DT seem like things that would just cause confusion because everything else is mostly "hack" utilities or visualizers that most people won't care about until much later, if at all. It's true that LNP comes with some stuff like dfhack but when I downloaded LNP I just ignored that stuff at first and basically just used LNP to try out graphics sets. I suspect that this is what most newbs would do should they feel motivated to mess with it. LNP doesn't really try to force that stuff on you.. its just sort of there if you dig for it.
So I basically tried to reorganize the doc flow for newbs based on what I would have wanted to experience when I first started playing, and things other people have said like "well finally I eventually heard about Dwarf Therapist [and wish I had heard of it earlier]." I also know of people specifically saying that they probably wouldn't want to try the game without a graphics set.
So anyway, graphics sets seem worth mentioning right away. DT could probably be removed, but in case someone goes Install->Tutorials->some-tutorial-other-than-the-quickstart-that-doesn't-mention-DT then mentioning it on the install page helps ensure that they at least see something about it before potentially getting stuck on the labor config UI.
I agree that third-party packages don't belong on the main wiki page but I don't sense that much confusion from anyone by mentioning them on the install page. If anything, perhaps the difference between "SDL" and "Legacy" is more confusing and should be explained if only to say "you probably want the SDL version".