And since one of the main reasons of using an IDE is to debug code, I decided I would start there.
Drop to Frame. I just discovered this one recently and it makes debugging so much easier. In the debug window if you right click the point where the Thread is suspended you see a menu option Drop to Frame. Its not clear from the name what it does but if you are stepping through the code and want to go back it drops to the beginning of the stack frame. The eclipse notes that not all VMs will support it, but if it does it saves me so much time when I step past my breakpoint.
Variables Window. This window is probably the most known, you can see all the variables declared. Some people seem surprised that you can even change the value of variables on the fly here.You can also navigate to the variable type and declaration. There are other options on the view menu for things like showing constants or references.
Display Window. I can't understand why this is not loaded by default, but its not. So go to Window->Show View->Other and Search for Display. I like it because I can use intellisense, inspect variables and even execute code, and then copy and paste working code back into my IDE.
These are just a few of the ones I think are useful, I'm sure there are many more. If you know of any other useful ones feel free to share it in the comments.
Also I'm using Eclipse Juno for this and if you want more details on some of these views or features of the IDE the Eclipse Reference Docs is actually pretty good.