Codemodder and SpongePowered Mixin cater to different scenarios. Codemodder is ideal for transforming source code you own, based on specific patterns. Changing source code allows the changes to be tracked, reviewed, and analyzed using standard tools like compilers and static analysis. It's great for large-scale codebase refactoring.

Contrastingly, SpongePowered Mixin uses Java bytecode manipulation, to transform the bytecode of a specific type. Bytecode manipulation comes with added risks and complexity, so this method is typically reserved for when you need to change the behavior of some external library or framework type. For example, Mixin is useful in Minecraft modding, because it allows modders to change the behavior of externally defined Minecraft types.

In essence, choose Codemodder for large-scale refactors to your source code, and Mixin to modify the bytecode of external Java types.