refineries work really well with adjancencies. I wouldn't. Use them isolated.

It also depends on the tech.  Pretty much all races have buildings better than durantium refineries at the age of war, giving much better than the +2 adj bonus from the refinery.  In early game without that tech, then yes, refinery is better.  But if its not an extremely low pop world or you have the tech (including better food, approval, and terraforming techs to get that pop up), then I would say the refinery has outlived its purpose.  Not worth it IMO as an isolated building, but can be in certain situations.

The answer depends to some extent on what you have, but the truth of the matter is that it is almost always worth building a hub structure, as long as the hub structure is one of the ones that doesn't consume strategic resources and the world you're considering building it on is appropriate (i.e. don't bother with Financial Sectors on lab worlds; power plants, on the other hand, might be worthwhile as, aside from the Solar Power Plants, they're relatively cheap for the bonus provided by comparison to standard factories). Research Coordination Centers are at least as good as labs so long as they're next to at least -5/-4/-2/1/5/10 Research Labs/Xeno Labs/Research Institutes/Research Centers/Research Academies/Discovery Spheres, Innovation Complexes are at least as good as labs so long as they're next to at least -5/-4.5/-3.5/-2/0/2.5 Research Labs/Xeno Labs/Research Institutes/Research Centers/Research Academies/Discovery Spheres, Solar Power Plants at least as good as factories when they're next to at least 0/1/3/6/10 Basic Factories/Xeno Factories/Mega Factories/Manufacturing Centers/Industrial Sectors, Fusion Power Plants are at least as good as factories so long as they're next to at least -2.5/-2/-1/0.5/2.5 Basic Factories/Xeno Factories/Mega Factories/Manufacturing Centers/Industrial Sectors, Quantum Power Plants are strictly superior to any of the baseline factories, and the economic hubs are strictly superior to any of the baseline markets.

Basically, so long as

[hub basic bonus] - [basic structure basic bonus] + [levels gained by using hub instead of standard structure] * [level bonus] > 0

the hub structures are worth using. Be careful applying this formula when the hub and basic structure it replaces do not provide the same bonus, as it the case for Durantium Refineries and Thalan Hives which replace basic factories but provide production bonuses rather than manufacturing multipliers.

As for when Thulium Data Archives are worthwhile? At best, the early stages of the game; a Thulium Data Archive must be adjacent to at least 0/1/3/6/10/15 Research Labs/Xeno Labs/Research Institutes/Research Centers/Research Academies/Discovery Spheres in order to be as good as another lab. I wouldn't bother wasting Thulium on the archives; the survey modules seem a better deal to me early on, and by the time you have standard survey modules the archives are well on their way to being detrimental rather than beneficial. Plus, the difference between an Archive and a Research Lab is fairly minimal; you only get 1 extra level per adjacent research structure, and each of those levels is worth only +0.05 to the research multiplier, and it only gets worse as the labs are upgraded.

The above section is based on the numbers for v1.03; if the numbers have changed in v1.1, then the conclusions may no longer be valid.