Important question, to me at least!

playing minor over major will give a dark mood, but it'll work since it's in the same key sig. playing major over minor might not work if it's not in harmonic or melodic minor.

Basically the music will set a mood that can change sometimes, and fits some kind of scale formula. If the tonal center of a song is B major than B major scale would sound really good because it would fit note for note. But you could play a B minor scale and it would be a little different but still work. It will sound kind of bluesy. You can also use any other B mode but you have to really know what your doing with those to sound good (especially if the chord progression was suggesting B major).

Now if you tried to use your G#minor scale it would sound great because it has the same notes as B major. They have different intervals though, if you dont already know the interval structure of the scales, that is the key to really knowing when to play what notes.

But then ive just made a song where the rhythm parth plays a little Dsus2-little riff and eventually it goes F5 G major D sus2. So the notes fit into the key of C major, but the tonal center of the song is Dm. So the Dm dorian scale sounds really good and is easy to use over it. You have to look at the music to decide what would sound best to play over it.