Well, I solved half your problem -- the 'javascript:' part.
The other half of the problem, the adding of your board URL to the front is being done by your browser. If you look at the actual page source (the HTML), you will see that the link looks like this:
<a href="javascript<b></b>: popUp('http://everydayjones.com/msgboard/calendar.php?do=getinfo&e=2&day=2004-9-30&c=1')">The Swiss Pub, Tacoma WA</a>
Since it looks like relative link to your browser (i.e., does not start with something like "http://"), it is adding the current page's directory (http://www.everydayjones/com/XXX) in front of it when you click the link.
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