IDE: Eclipse. IBM's poured $40 million (so far) into this IDE, and
made it free. Rename/move methods/classes/packages, even across
projects! Seamlessly work on multiple projects; fast smart
compilation; native GUI; specialized window-layouts ("perspectives");
plug-ins; ...

Text editor: XEmacs. Macros, built-in psychoanalyst:-), literally 1000
plug-ins, including: view/edit lines matching regexp, text stats, no
mouse needed, highlight regexp, run shell command on selection,
language-indep auto-complete, multiple window-layouts, saves state
between sessions, random sort, ...

Code-coverage testing: JCoverage. Produces some beautiful HTML pages
with red/green bars, linked to your source code in HTML.

Code comprehension: Doxygen (works for Java). Produces beautiful
flowing class/interface-hierarchy diagrams, each linked to your source
code HTMLized.

Code metrics: CCCC (works for Java). Generates a huge HTML report
containing a ton of useful metrics, including: lines of code,
fan-in/fan-out (cool!), depth of inheritance tree...

Finding unused methods: Proguard. An obfuscator, but has an option to
find dead code.

Chart library: JFreeChart. A library (jar file) rather than a
development tool, but hey, it gives your app slick-looking graphs!
Comes with easy-to-understand examples.

Jon