There are likely more secrets than are listed here
In the Intro of the game where it shows you ConcernedApe`s Logo , Click on it and the glasses will pop/eyes will open and you will hear a duck/splat sound.
In the title menu of the game , if you repeatedly click on the "E" Letter of the word "Stardew" , an alien opens the "E" like a door and starts waving at you , until after 2 seconds it fades away.
If a Super Cucumber is taken and used on the brown box located inside the fenced area north of the Blacksmith, The Player is rewarded with a statue 32px ??HMTGF??.