The word ‘good’ in the English language is a very nebulous word, and can be used a number of ways.
Good is often used as a generic positive word, as in ‘that’s a good cake,’ or ‘I read a good book.’ The word good in those cases means something different in different contexts; ‘good cake’ might mean ‘well-made’ or ‘tasty’. Likewise, a ‘good book’ is probably a ‘well-written book’ or what’s called a ‘page-turner’. In these cases ‘nice’ is approximate.
However, in the cases you’re talking about, good is being used more to emphasise the word after it, with a bit of a positive connotation thrown in. ‘Nice’ has the same meaning in that second group of sentences. ‘Good long talk’ or ‘nice long talk’ in those sentences could be replaced with ‘very long, pleasant talk’, like
We just had a very long, pleasant talk.
I had the pleasure to sit down a few weeks ago for a very long, pleasant talk with...
Ditto with the third group of examples, although the comma in those lays a little more emphasis on the length of the talk, as opposed to the ‘goodness’ or ‘pleasantness’ of it, and it can even sound slightly menacing, depending on context.
Your first sentence of the third group is actually a very good example of that. Can you imagine a mob boss muttering to someone he’s just captured who’s still struggling and thrashing “I’d like to have a good, long talk with you once you’ve calmed down”?
Hope that helps!