I've never done any certificate courses on-line, but many years ago I did enroll in a couple of correspondence courses. Both courses granted certificates of training once the course was complete. The pharmacy tech course certificate would not have let me work in a civilian pharmacy, but it was accepted by the National Guard and allowed me to be in charge of ordering and doing the inventory for our medical unit. The environmental course I took wouldn't have been accepted for the education needed for probably 98% of jobs - although it did help me be a few steps ahead when I went to college for the same major.
Those were two examples and every place that offers the courses have different levels of accreditation. If you plan on taking courses related to your current career (for advancement opportunities, etc), talk to your personnel representative and he/she should be able to tell you if the company will accept that course in place of regular college courses or other training. If you plan on using the course in order to change careers, you should discuss them with people currently working in that field. Even if places don't accept the certificate, you would still possess new or improved skills or knowledge which can help you during interviews or on-the-job training sessions which may help with promotions.
Most important is not to rely on what any of the places offering the certificate programs tell you. They may tell you their certificates are accepted by most major corporations or service providers in place of regular college courses and that not really be the case. Always check with the places you may be thinking about working (or currently work) so you know for sure. Then again, if you're doing for self-improvement, free is always a great price.