While most of them are Easter Eggs, Dexter's Lab and Powerpuff Girls always seem to take place in the same universe to me. There's even an episode where the PPG team up with Major Glory, along with Val Hallen and a bunch of other super heroes, which goes beyond just a simple cameo and outright saying that it's a shared universe.
Then you have small things in the Powerpuff Girls, (Dexter cameos aside), like a Quackor cameo or Bubbles and Dee Dee having the same imaginary friend.
As for Samurai Jack, I think it could possibly take place in the same universe if you view it like Back to the Future 2: when Aku sends jack to the future and he reigns over the planet for centuries, this would be one alternate reality where it's very possible that neither Dexter nor Professor Utonium (and by extension the Powerpuff Girls) are ever even born.
If we were to ASSUME that Jack does eventually go back to his time and successfully defeat Aku, then reality would return to normal and centuries later Dexter and the PPG would be having their adventures in modern times.