I have it wrong, don't I?
Yes. 
To start with, give your fading objects IDs. There's no need to use Javascript to store them. Like so:
Code:
<p id="inst0"><small><b>NOAA - CREST</b><br><br>CREST is a collaboration among institutions to educate and train students in the field of environmental remote sensing by conducting research consistent with NOAA\'s Science Mission of Environmental Assessment, Prediction and Stewardship by bringing together:<p><li>The City University of New York campuses:<ul><li>The City College of New York</li><li>Lehman College</li><li>Bronx Community College</li></ul></li></p><p><li>also in cooperation with<ul><li>Hampton University</li><li>University of Puerto Rico at Mayaguez</li><li>Bowie State University</li><li>University of Maryland, Baltimore County</li><li>Columbia University</li></ul></li></p><p>CREST forms a broad-based research team in remote sensing, with research applied in Earth Atmospheric, Environmental and Marine Sciences. </small></p>
Then, for your menu, we'll want to define a new function to fade out all the old ones, and set up all the initialization stuff:
Code:
<script type="text/javascript" src="FadableObject.js"></script>
<script type="text/javascript">
function hideAllItems() {
for(var i=0;i<FadableObject.fadeThreads.length;i++)
FadableObject.fadeThreads[i].fadeOut();
}
onload = function() {
FadableObject.init();
var c;
for(var i=0;c=document.getElementById("inst" + i);i++)
new FadableObject(c, 3, 10, 0, 99, true, false);
}
</script>
<div id="scriptmenu" style="line-height: 20px; vertical-align: top;"><strong><br>
<a href="noaa" onmouseover="hideAllItems();document.getElementById('inst0').fadeThread.fadeIn();" onmouseout="document.getElementById('inst0').fadeThread.fadeOut();">NOAA - CREST</a>
<br><br>
Without any of the green bits, the code will function as I think you were trying to get it to in your attempt above. If you add in the green bits and remove the red bit, the user won't need to keep his/her mouse over the item for the text to be shown.
One day someone colour-blind is going to ask for help, and then we'll be stuck.
Ah well.
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