There is a secret door in the Weaver’s Den area that shows the Seal of Binding, which appears in only a few other areas. The Seal of Binding was finally explained in the second free DLC pack, The Grimm Troupe.
There is a secret area called the Shrine of Believers. This is the place where all of the messages from Kickstarter backers are displayed. You can inspect them to read the messages.
By destroying the sign in the Infected Crossroads, then leaving and charging down the well, you’ll be able to kill Menderbug and enter his house, where you can read his diary entries.
The Dung Defender has a secret room that you can enter by breaking the ground above it, although the ground isn’t marked. Inside, you can find his statues and also see him sleeping. He mentions Isma in his sleep, suggesting that there was once a close relationship between the two characters.
If you talk to Elderbug while you have the Delicate Flower, he asks if you brought it for him. It is possible to give it to him, which overjoys him and makes him happier about the world. He promises to take good care of the flower so that he can enjoy it with you when you return.