After discovering that I could configure OneNote to stay on top of other windows I found it was a really great way to take notes on a document. The problem I next encountered was that for the type of note taking I was doing I would prefer to use Mind Manager 7.
Unfortunately, MindManager does not appear to offer this functionality. However - a quick Google revealed a great little free utility that will let you keep one or more windows on top. The application is called XNeat Window Manager - here is an out take from the site:
XNeat Windows Manager adds additional features to the Windows taskbar and system tray, that enables you to minimize any window to an icon in the system tray (instead of the taskbar), keep any window on top, set a custom transparency level, and also hide any window or tray icon, furthermore the program allows you to re-arrange the order of the taskbar buttons by simply dragging them around. XNeat Windows Manager integrates into the right-click menu of the taskbar and system tray. It also allows you to change the taskbar appearance by hiding the Start button, system clock and other elements.
For want of a better term - Neat! Works exactly as it says and I was soon note taking in Mind Manager while reading a document in another window behind it.