PDF link does not open in IE, but will open in Firefox and Safari.

Dreamweaver code:
<li><a href="javascript:; "         onClick="MM_openBrWindow('resources/facultyresources/SAFunctionalFramework.pdf','toolbar= yes,menubar=yes,scrollbars=yes,resizable=yes,width=550,height=450')">Eliciting and Assessing Performances of Self Assessment</a></li>

How PDFs open when clicked on is controlled by the user's settings. You can't use code to force them to display in-browser.
Check your IE security settings, especially if it's a local file that won't open. IE has some idiotic security settings when trying to open local files.
If the site has been uploaded and IE won't open the PDF, you will want to make sure you have the Acrobat plug-in installed and that it's set to be used from within IE's settings.

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