When you take Thor and Hercules, for instance, you're dealing with two, virtually identical characters in terms of physical attributes...who is more powerful...Yup, Thor is.
Even if Thor's other powers were more limited, say able to create a flashlight from his finger, he'd be more powerful than Herc...though the difference in that case wouldn't be enough to make a practical difference.
Now, take one and make them 5% weaker...the other is more powerful. But give that other one flight...now is it about equal again...maybe depends on speed and quality of flight when compared with effectiveness of leaping ability....
It gets complicated quickly...I will say that if you have someone who has EP as powerful as Hercules' punches, they're not as powerful as Herc because they'll lack his durability....though they can attack at range more easily which makes up for it somewhat...so maybe his EP is somewhat more powerful...to the point we agree that person and Herc are equal in power....
THEN, combine the powers into one person...I don't think that person is twice as powerful as Herc, but he's clearly more powerful...how much is harder to measure.
With Superman and Thor, I think a pretty good argument can be made that Post Crisis Superman may not have been as strong as Thor up through Return of Superman, and the converse was a harder sell (though roughly equal is a reasonable conclusion)...after return of Superman, Supes seemed to have better showings relative to a lot of his previous peers and enemies, though top end comparables still seemed to be equals (and a whole issue to establish Superman and CM as equals in every way after that point), but a reasonable evaluation could range from peers to Superman having a slight advantage in strength.
Superman has more hard durability, but overall not a big durability advantage. Superman also has a speed advantage.
IMO Thor's energy and other powers have proven more impressive and significant than his physical attributes, and I think they are greater than Superman's combination of abilities by a fair margin. Physical attributes Superman probably has an edge, other powers, I think Thor has a substantial advantage.
Now, the way they actually fight, I think puts Thor vs. Superman as a very even fight, and it is reasonable to conclude Supes would be the favorite (I don't necessarily agree, however), but Thor tends to fight a fight that plays to Superman's strengths. Surfer, OTOH, i think would be a clear favorite vs. Superman, and Thor remains a favorite vs. Surfer.