My Problem: When programming an application or learning a new programming language using a PDF eBook, I usually have to switch back and forth between applications just to read the PDF. This takes up a lot of my time trying to learn a language. A book I have to keep moving my head to look at the book and what not. The windows won't stay put or scale with the IDE (you have to do it manually I understand). But still if you read the PDF and start to type it switches focus to the pdf so you have to click back on the editor.
I know what you mean but, if you're working in eclipse you probably don't want it to have to share screen space with anything. This is where multiple desktops/screens comes in v.handy - PDF on one screen, eclipse on an adjacent one, quick keyboard shortcut to switch between the two - this works for me at least.