After messing up with some application requiring a huge number of ajax calls, I ended up thinking about this little piece of code:

window.onload=function(){
Event.observe(document.body, 'click', function(event) {
    var element = Event.element(event);
    if ('A' == element.tagName){
        if ($(element.target) != undefined){
            new Ajax.Updater(element.target,element.href,
            {method:"post",evalscripts:true})
            Event.stop(event);
            }

        }
    });
}

basically, this 10-line worth trick sets an event listener on every click. If you click on a ‘a’ with a target attribute set up, it starts an Ajax.Updater call on it.
you can of course add GET parameters and feed .php, and of course javascript code is parsed as well..
the complete seed [just a .htm and .php example file added] can be downloaded here