I have three monitors, so I usually run with this configuration:
- Left Monitor: documentation / ebooks.
- Middle Monitor: code / debugging
- Right Monitor: Test application / scrolling logfiles (if needed)
This usually works pretty well, and since the monitors are fairly big I rarely need to use the test application in full-screen, so there's plenty of room for my tail -f windows.
I also use AutoHotkey to assign hotkeys that flip to the most important windows, like Firefox or my SSH session. That way I can simply use a shortcut key to access them when necessary.
The left monitor is actually a separate computer running Linux and keyboard/mouse shared with Synergy, so I have multiple ebooks or documentation pages open, one on each virtual desktop... I can flip between the documentation by moving my mouse to the left and using a shortcut key.