I pretty much spend most of my time in Eclipse and at the command line.
With Eclipse I usually modify the keyboard bindings so I have features such as Open Type/Resource, Quick Outline, Show Refactor Menu and so on at the tip of my fingers. I also install Q for Eclipse to enable good Maven-integration allowing me access to the source of my dependencies when coding.
At the command line it's tools such as Maven, Ant and Subversion that are used the most. I have a few commands to switch between JDKs to test that projects compile and run on all their intended targets.
I used to keep a copy of JAD around, but thanks to Maven and Q for Eclipse I harldy ever use it anymore. Decompiled code is not nearly as usable as the original.
I almost forgot, JConsole helps with monitoring your application also I use YourKit for more advanced profiling.