I'm late to the party as usual but nevertheless:
Although "ja" & "ning" are often used interchangeably they can be used to group words within the list, to indicate their interrelationships. For example, if you have 4 people coming to the meetup then you could say:
1) Tulevad Mari, Jaan, Marge ja Jaanus.
2) Tulevad Mari ja Jaan ning Marge ja Jaanus.
The difference is that in first case you just list all those people who come but in second case you say that "Mari ja Jaan" will come and also "Marge ja Jaanus" will come. Second sentence gives the hint that Mari & Jaan belong together (either they're a couple or you just know they come together on this occasion) and also Marge & Jaanus belong together. So you're really saying that:
Tulevad (Mari, Jaan) & (Marge, Jaanus).
This is best used in short sentences, when used with long list it may confuse the reader instead of clarifying the matter. Problem is that different people have different view on whether the grouping occurs at "ja" or at "ning". For example, if the sentence is written:
Tulevad Mari ning Jaan ja Marge ning Jaanus.
Then some people would group it this way instead:
Mari & (Jaan, Marge) & Jaanus
In this sentence it doesn't really matter but I've seen sentences where I had to think for some time before I understood what exactly it meant. I don't remember any shining examples at the moment but I do remember spending about fifteen or more minutes once discussing with others whether we should use "ja" or "ning" in one particular sentence in order to guarantee that the reader would understand it exactly as we meant it.
But yes, in general, they're freely interchangeable.