Mac OS X Hints today published a simple one-liner to prevent Help Viewer windows from floating above everything else on the screen. Open a Terminal window and paste the following line:
defaults write com.apple.helpviewer NormalWindow -bool true
This undoes one of the worst design decisions Apple made in the latest version of OS X: To force the Help windows float over everything else on the screen. Reverting to the unloved default behavior is as simple as changing the 'true' to 'false' and executing the line again.
Floating windows are not inherently bad: Applications use 'em to contain tools or display things you may use in more than one window, so that, for example, your Photoshop brushes stay in the same place on your monitor no matter which image you're editing. What makes the floating Help Viewer window bad is that it attempts to overlay everything in every app, ubiquitously. Unless you have screen real estate to burn, the Help Viewer actively prevents you from both doing a task and reading how.
Help Viewer doesn't remember where you were and it doesn't allow bookmarks. Closing the Help window means re-navigating to where you left off, a lot more work than simply putting it in the background and foregrounding it again a moment later. So thanks, Mac OS X Hints.