Any ideas on how to make a link in a link webpart open in a new window? Thanks in Advance
I assume you mean you have a list web part and it contains Link content type. You wish the Link content type to open in a new window. My only suggestion is that you use a custom XSLT for your List WebPart and render the xhtml link tag with a target attribute.
I'd go with jQuery. Get all links in the webpart and add the target attribute:
$(document).ready(function(){
// selector: get all links in the link webpart, check for unique (parent) class
$('selector').attr('target', '_blank');
});