Optimizing a JavaScript snippet for portability and readability
I would make it less compact to improve readability.  Leave it up to your build process (minifier) to make things compact.  Your goal should be to make things understandable.

Use regular expressions

In cases like this, where you have a strict format, I love using regular expressions:

/** @const */
var TIME_FORMAT = /(\d{2}):(\d{2})/;
...
"10:30".match(TIME_FORMAT) // == ["10:30", "10", "30"]


This makes it clear that you expect a date to consist of two digits a colon, and two more digits.  As a bonus, let everyone know it's a constant with JSDoc and common coding conventions.

Define functions

Short modular code is easy to read:

/**
 * Parses a time string and returns the hours and minutes.
 */
function parseTime(text) {
    var match = String(text).match(TIME_FORMAT);

    if (match === null) {
        throw new Error('Time "' + text + '" could not be parsed.');
    }

    return {
        hours:   Number(match[1]),
        minutes: Number(match[2])
    };
}

/**
 * Gets the total minutes of overtime based on time worked and number of working hours
 * in a day.
 */
function calculateOvertime(parsedTime, workingHours) {
    var minutesWorked = parsedTime.hours * 60 + parsedTime.minutes;
    var minutesRequired = workingHours * 60;
    return minutesWorked - minutesRequired;
}


Here, the parseTime parses the time, returning an object, and calculateOvertime calculates the overtime.

Put it all together

Putting it together, your actual function does become more compact and more readable because tangental functions are extracted:

/**
 * Gets the total minutes of overtime from a tracking table.
 *
 * @param selector A CSS2.1 selector, DOM element or jQuery object pointing to the
 * tracking table.
 */
function getOvertimeFromTable(selector, dailyWorkingHours) {
    var totalMinutesOfOvertime = 0;
    var $dailyTimes = $(selector).find("font:not(:empty)");

    $dailyTimes.each(function () {
        var parsedTime = parseTime($(this).text());
        var minutesOfOvertime = calculateOvertime(parsedTime, dailyWorkingHours);

        totalMinutesOfOvertime += minutesOfOvertime;
    });
}

alert('Overtime so far: ' + getOvertimeFromTable('.links', 8) + ' minutes');


Protecting global, enabling compilation

Right now we are exposing a variety of variables and functions on the global object.  This means that anyone could call parseTime or read a similar function.  It also means a minifier can't rename the function to a shorter name.  Wrapping everything in a closure will be the final step for making sure your output code is more compact and your source needn't be:

/**
 * Alerts the number of hours of overtime you have accumulated so far in this pay cycle,
 * assuming a standard 8-hour day.
 */
(function () {
    /* Your code here */
}());