Don't use regex to parse HTML. [X][HT]ML is not a regular language and cannot reliably be processed using regex. Your browser has a good HTML parser built-in; let that take the strain of working out where the tags are.
Also you don't really want to work on html()/innerHTML on body. This will serialise and re-parse the entire page, which will be slow and will lose any information that cannot be serialised in HTML, such as event handlers, form values and other JavaScript references.
Here's a method using DOM that seems to work for me:
function replaceInElement(element, find, replace) {
// iterate over child nodes in reverse, as replacement may increase
// length of child node list.
for (var i= element.childNodes.length; i-->0;) {
var child= element.childNodes[i];
if (child.nodeType==1) { // ELEMENT_NODE
var tag= child.nodeName.toLowerCase();
if (tag!='style' && tag!='script') // special case, don't touch CDATA elements
replaceInElement(child, find, replace);
} else if (child.nodeType==3) { // TEXT_NODE
replaceInText(child, find, replace);
}
}
}
function replaceInText(text, find, replace) {
var match;
var matches= [];
while (match= find.exec(text.data))
matches.push(match);
for (var i= matches.length; i-->0;) {
match= matches[i];
text.splitText(match.index);
text.nextSibling.splitText(match[0].length);
text.parentNode.replaceChild(replace(match), text.nextSibling);
}
}
// keywords to match. This *must* be a 'g'lobal regexp or it'll fail bad
var find= /\b(keyword|whatever)\b/gi;
// replace matched strings with wiki links
replaceInElement(document.body, find, function(match) {
var link= document.createElement('a');
link.href= 'http://en.wikipedia.org/wiki/'+match[0];
link.appendChild(document.createTextNode(match[0]));
return link;
});