Opeth's scales are more or less free-form from a listening standpoint, but if you really want to look at it closely...
They use a combination of the melodic minor (many songs with a heavy emphasis on the major seventh)
They also use the fifth mode of the harmonic minor scale, the phrygian-dominant, also known as the spanish gypsy scale. This scale gives them that minor second, as seen in the opening theme in Master's Apprentice or The Grand Conjuration.
To arrive at a sound like theirs, you would be best off learning the harmonic minor and the phrygian-dominant, and improvising with a lot of chromatic motion. If you look at songs like Blackwater Park, you'll see a few riffs with up to 7 consecutive notes, which you won't find in any scale.
Opeth tends to be free in writing music that contains almost every note of the chromatic scale, but the major third is something you'll rarely see unless they're "skipping" over it very quickly, while playing a chromatic movement or playing in a phrygian-dominant scale, in which case the major third up from the tonic gives more-so a sound of a raised leading tone (since it's the fifth mode of the harmonic minor).
But really, at some point, music goes beyond scales and theory, and you're better off just playing what sounds good. I, for one, have no creativity, and must resort to theory to create anything half decent
Hope this helps
:Smokin: 
