Nope, not all of them. There's only one secret encounter I found so far, and honestly it was before I started hunting for other secrets. What I'm doing now is replaying all the levels to see if anything interesting pops up, but either they're harder to find or I'm completely looking over them (or clues that lead to them). I suggest playing the entire game, getting all upgrades (and weapons of you can), stack on lives, then redo the levels. There might be a easier method, but it's what I'm doing right now.