When I am in a .java file, the unused code is usually grayed out or has a green underline saying this code will probably (probably because of some weird JNI/Reflection corner cases) be unused. But I have this project with thousands of Java files and I want to find all instances of such probable-unused code. How can I do that in IntelliJ IDEA?
Just use Analyze | Inspect Code with appropriate inspection enabled (Unused declaration under Declaration redundancy group).
Using IntelliJ 11 CE you can now "Analyze | Run Inspection by Name ... | Unused declaration"