I believe in one part it's somewhat implied the question is "What is 6 times 9?", which is silly considering the answer is wrong.

The programming joke goes something like this:

  #define SIX 1+5
  #define NINE 8+1
  return SIX*NINE;

That's on IIRC the Earth 2 in its very early existence and Arthur and Ford start pulling scrabble letters from the bag...

I guess it has a few million years to run to resolve to the correct question. :)

Presumably the mice would then require a third supercomputer to tell them why this is the most important question of life, the universe, and - you know - everything.

Isn't it also implied that the question was wrong because humans weren't supposed to land on the earth in the first place and serve as a bug in the calculations?

The reason the question came out wrong is because Arthur is descended from the Golgafrinchans, not the native ape-men, i.e. the program was corrupted early on.

The miniseries ends with that reveal, and Arthur quips “I always knew there was something fundamentally wrong with the universe.”

Yes it is; in base 13. :-) [1]

[1] http://www.6times9.com/

So, there may be a real, meaningful question which result is 42, when using a different "base" to view the question at?

I think it's more poetic to view it as the question for the meaning of everything has a wrong answer to it.

It doesn't make sense, the universe isn't specifically obligated to make any sense, so why should the ultimate question and answer?

'I may be a sorry case, but I don't write jokes in base 13.' - Douglas Adams

By coincidence mostly.

Are you saying the improbability of that approaches infinity?

Well, on yet another level, isn't the universe - at least, as far as it's limited to our own human condition - all about wrong answers?

In the TV show, near the end you can just about hear the strains of Bob Dylan singing "How many roads must a man walk down....".