I remember when playing each Monkey Island on release (with the exception of the Tales of Monkey Island) - and in each of the first 4 games I always remembered "knowing the secret of Monkey Island".
During the end of the first game I assumed it was the fact the undead LeChuck was hiding with the catacombs of a giant monkey head. I didn't think there was anything to suggest the secret was anything more complex or yet unexplained after finishing the first game. The game had an ending and there was nothing to suggest the story would continue after the demise of LeChuck.
When I played the second game, I had no doubts about my conclusions for the first game until the end when LeChuck reveals himself as your brother (and everything in the two games was a fabrication). I remember still thinking that the secret was the way LeChuck was hiding on the island - but because now everything before wasn't real it didn't matter what the secret was. When talking to others after playing the second game some believed the real secret was actually Big Whoop (although I didn't come to the same conclusion).
The Curse of Monkey Island made an arguably weak explanation of events between the second game and the start of the third game. However, everything previous was thrown out when Guybrush asks LeChuck for the secret of Monkey Island - as if the secret was in fact never explained before.
The fourth game is explicit in that the monkey kombat is the real secret.
Remember, by the time the first three games were released the internet was not like we know it today. It seems to me that the on-going notion of the secret never being explained has become a running joke fuelled by online debates, when in fact there was no problem during the first 2 games.
Conclusion
The secret was the fact an undead LeChuck was hiding under the monkey head (implied).
This then changed during the series to the fact the giant monkey head was part of a robot (explicit).
The asking of "what is the secret of Monkey Island" became a running joke perhaps from the third game, and continues beyond the fourth game (despite the explicit revelation).