Seems like a reasonable way to do it… I’d just suggest that you make use of jQuery’s data storage utilities rather than introducing an extra variable (which could become a headache if you wanted to keep track of a whole bunch of links). So based of your example:
$('a').click(function() {
var clicks = $(this).data('clicks');
if (clicks) {
alert('odd number of clicks');
} else {
alert('even number of clicks');
}
$(this).data("clicks", !clicks);
});