If you're familiar with using TODO tags in Eclipse, a simple step up would be to use Mylyn. At it's most basic, it's a simple todo list. But, it also associates context with tasks - click on a task to activate it, do some stuff, and then next time you activate it, Eclipse will open up the relevant classes, and show you the relevant methods. Even more powerfully, if you eventually move to some other bug tracking system, Mylyn can pull tasks from those systems and present them in your IDE.

Most Eclipse downloads these days have Mylyn bundled in as standard. Just search out the Task List view and start adding tasks.