dir="auto" JavaScript shim for IE
My 2 cents:


Code looks really good overall
In prependOverride, the naming is unfortunate

The parameter isLTR is really what you request, not what it is
The var direction really is a boolean, not the direction of the element
If you are going to /** type **/ variables, you might as well go Spartan and use e instead of element

prependOverride has 4 magical constants 
isLTR should cache the regex, not rebuild it in every call 


for prependOverride the following might be cleaner:

function prependOverride(/*HTML Element*/ e, /*Boolean*/ requiresLTR) {
    var hasLTR = getDirection(e) === "ltr";
    if (hasLTR !== requiresLTR) {
        e.innerHTML = (requiresLTR? "&amp;#8237;" : "&amp;#8238;") + e.innerHTML + "&amp;#8236;";
    }
}


or, even you could pass the direction you require

function prependOverride(/*HTML Element*/ e, /*String*/ requiredLTR) {
    var actualLTR = getDirection(e);
    if (actualLTR !== requiredLTR) {
        e.innerHTML = (requiredLTR=="ltr"? "&amp;#8237;" : "&amp;#8238;") + e.innerHTML + "&amp;#8236;";
    }
}


I will leave the naming of the magical constants to you.