Well I havent found so many secrets in games so the list is quite short for me.
Dungeon Siege 2: The secret realm of game developers. My inital reaction was: Waaaaaaaaaaaaat is this Madnes?!
The reason why this secret is memorable for me is due to the amount of work it is required to enter the realm.
The flute in Super Mario Bros 3. This little item was god-sent for me as a kid. I wasnt so good at platformers at that time so this item helped me get to levels I havent been to.
Any other secret I have forgotten about over the years..