Open Excel files in new window
I've had this problem too. Here's what I did:
In Excel 2003, go to Tools -> Options -> General tab.
Make sure the option, ‘Ignore other applications’ is checked.
In Excel 2007 & 2010, Click the Office button -> Excel Options -> Advanced.
Under General, check ‘Ignore other applications that use Dynamic Data Exchange’.
I don't know why this isn't built in. Source: http://www.lytebyte.com/2008/05/13/how-to-open-two-excel-files-side-by-side-in-separate-monitors/
It's a bit back to front, and will work for any program not just Excel, but I middle-mouse-button click the Excel icon in the Windows 7 Taskbar and create a new instance of Excel, then open the documents in each instance of Excel.
Once your have multiple instances of Excel running you can arrange them side by side by holding down Shift and right clicking on the icon:
There are certain disadvantages to having all your workbooks opened in different windows. For one thing, if you write a formula in one workbook which references another, it will include the full file path of the other workbook. For another, copy/pasting from one workbook to another reduces the number of options available for the destination data, like keeping the column widths, etcetera. It's possible that for your purposes those things won't matter much, but basically if you experience any "weird" behavior when using multiple workbooks in multiple windows, you might try opening them in the same window to see if the weirdness goes away.
My preference is to leave the default behavior to open Excel workbooks in the same window, and when I want individual workbooks opened in different windows I right-click the file and select "Open in new window". In order to do that, I wrote this small utility. It's free. Feel free to install it.