Some of the collectibles have changed from the original (aka switched to a new location), so I have made a new video for the Definitive Edition.
There are a total of 15 Energy Cells, 12 Life Cells, 33 Ability Cells, 12 Spirit Wells, and 9 Map Stones in the game. There are 45 Secret Areas.
Seasoned Explorer unlocks after finding 23 of them, and No Stone Unturned unlocks after finding all 45. Below is a video showing every collectible in the game including Secret Areas, in chronological order according to the earliest you can obtain them. I suggest waiting until you have Stomp to go to Black Root Burrow as you need it to access the lower area.
For those that prefer a vid with just the secret areas: