Place twelve 2 1/2-inch baking liners on a baking sheet. In a double boiler, melt the chocolate. Reserve the pot of hot water to keep the chocolate liquid, as necessary.
Place about 2 teaspoons of the melted chocolate in a baking cup, swirling to coat about halfway up the side of the cup. Repeat with the remaining cups. Refrigerate until set.
Using an electric mixer, beat the butter until fluffy, about 2 minutes. Beat in the peanut butter and honey. Transfer the mixture to a resealable plastic bag and snip off one corner.
Fill the chocolate cups about three-quarters full with the peanut butter mixture, smoothing the surface. Refrigerate for 15 minutes.
Top each peanut butter cup with melted chocolate to enclose, smoothing the surface. Refrigerate until hardened. To serve, remove the candies from the baking liners.