Ubiquinone is the oxidized form of CoQ10 and is the more common form of commercially available CoQ10. It has been around for ages, and if you've ever bought one of the cheaper CoQ10 supplements, it has most likely been in the oxidized form. If the label doesn't specifically mention which form of CoQ10 the product contains, it's very probably ubiquinone.

Ubiquinone and Ubiquinol exist together in the body; the body converts ubiquinone into Ubiquinol. CoQ10 as ubiquinone is the "old" form of CoQ10 (by "old" we mean the form that has been commercially available for a long time). The Ubiquinol form is "new" in the commercial sense, and the form touted as being much more absorbable. Coenzyme Q10 exists in both Ubiquinol and ubiquinone forms, but they have vastly different roles to play in the body. For instance, Ubiquinol is an electron donor, while ubiquinone is an electron acceptor. The electrons that Ubiquinol donates neutralize free radicals. This fact alone makes Ubiquinol the form of CoQ10 that protects against toxic oxidative reactions in the body.

The chemical difference between ubiquinone and Ubiquinol is that the Ubiquinol compound contains two hydroxyl groups. These two hydroxyl groups enable Ubiquinol to be more "hydrophilic" than ubiquinone, and thus much easier to assimilate.
The term "hydrophilic" means readily absorbable or dissolvable in water. The two hydroxyl groups on the Ubiquinol compound result in its stronger bonding with water, which helps explain why it is so much more bioavailable than ubiquinone. Ubiquinol has far greater water solubility and much better absorption into the bloodstream after ingestion.

Ubiquinone is the fully oxidized generally sold commercially. Once ingested and absorbed in the body - more than 90% of the ingested Ubiquinone is converted into its "active" antioxidant form called Ubiquinol. More than 90% of the circulating CoQ10 in our body is present as Ubiquinol. The body has reductase enzymes which take the ingested CoQ10 in food and supplements and convert most of it into Ubiquinol. Research, (in animals and humans), has shown Ubiquinol to be absorbed better than Ubiquinone. Therefore, Ubiquinol afford an advantage over ubiquinone.

Ubiquinol, the pre-converted, active antioxidant form of CoQ10, offers the same important health benefits as CoQ10. Because it is pre-converted, Ubiquinol Q10 is ready for immediate use in those 40 and older, and those who have conditions associated with normal aging. This form of CoQ10 is the antioxidant form which neutralizes free radicals and decreases cellular damage. Ubiquinone does not have this antioxidant effect. Since the body converts ubiquinone into Ubiquinol, there is an extra step involved, and not all of the ingested ubiquinone gets converted into Ubiquinol. In healthy people, over 90% of the CoQ10 in the blood is in the form of Ubiquinol, but as you get older, both the total level of coenzyme Q10 and the body's ability to turn it into Ubiquinol decline. This doesn't mean that taking ubiquinone is ineffective; all it means is that taking ubiquinol is more effective. If you are in your twenties or thirties, your body can probably convert much of the ubiquinone into Ubiquinol, If, on the other hand, you are over forty or concerned about your heart health, it may be worthwhile to go for the Ubiquinol. Ubiquinol is already in its reduced form as a potent anti-oxidant. Ubiquinol inhibits protein and lipid oxidation in cell membranes, and helps to minimize oxidative injury to DNA.

Ubiquinol is up to eight times as effective as ubiquinone in increasing blood levels of Ubiquinol. So to get the same effect, you could take one eighth of the amount as Ubiquinol compared to ubiquinone.

Ubiquinol works better for congestive heart failure than Coenzyme Q10. One human study actually does show this claim to be true. (http://www.ncbi.nlm.nih.gov/pubmed/19096107)
Here is a recent case study received by Kaneka, the manufacturer of natural pharmaceutical grade Ubiquinol and ubiquinone:
A 65-year old gentleman with advanced ischemic cardiomyopathy was on maximal medical therapy. In June of 2006, he had low heart function and was receiving 450mg of a soybean oil-based CoQ10 that revealed a level that was sub-therapeutic. He was then given the Ubiquinol formulation at exactly the same dosage of 450mg per day. Three months later, in September of 2006, his CoQ10 level had increased dramatically. Further tests one month later showed a dramatic improvement in heart function and he no longer required any diuretics. By January of 2007, his improvement was great enough that he became quite active and required no further hospitalizations. The case study ended with the physician stating: "This single case represents very striking improvement that I have not seen before in 25 years of cardiology practice...We have now repeated and are continuing to treat several other patients with end-stage or far advanced congestive heart failure with similar remarkable findings."
This study demonstrates the importance of using Ubiquinol, especially as we age. Also, as demonstrated, Ubiquinol does not require the high amount needed by ubiquinone to gain the same therapeutic effect for certain conditions.

CoQ10 Level decreases as age increases                    Effect of Ubiquinol compared to conventional CoQ10(Ubiquinone)