What keys should I keep for later?

Solution 1:

The game has 11 different keys:

• Gardener's Key (3)
• Moonflower Key (3)
• Cavern Key
• Village Key (2)
• Old Service Key (3)
• Clockmaker's Key
• Bell Tower Key
• Graveyard Key
• Architect's Key
• Castle Key (3)
• Crypt Key (4)

You can use one gardener's key each in the ramparts, the graveyard, and the forgotten sepulcher to collect the moonflower keys. To take a route through all three of those places you need to have 3 active boss cells.

You need all 3 moonflower keys in high peek castle to unlock the blueprint "Acceptance".

You need the cavern key in the graveyard to open the path to the cavern. You only need to do this once.

The village keys are noteworthy, though not required in a different stage. There are 2 keys and 3 doors in the stilt village. 2 locked doors will block your way towards the end of the stage, where you will find a third door that you need to open to get the blueprint for the counter shield.

You can skip the first door by taking a secret path above it. Doing this allows you to take one of the keys to the third door

Read here for more information on keys.