My first thought was to suggest a tiling WM too, but you're on Windows - VirtuaWin (http://virtuawin.sourceforge.net/) gives many of the same benefits.

It gives you multiple workspaces and lets you configure keybindings for lots of UI events. I have alt+[1-9] and shift-alt+[1-9] set to "change to workspace N" and "move window to workspace N", respectively. At that point, muscle memory kicks in, your fingers know Emacs is always on workspaces 7 and 8 (or whatever), etc.

That'll make it easier to manage the tens of Windows that come from reading lots of papers side by side.