Aside from the MD, there are few differences between the two types of programs.
4-year residents typically spend 30-36 months on the OMFS service (the remaining 12 - 18 months are spent on Anesthesia, Medicine, ENT, Plastics, General Surgery, ER, etc.: it varies from program to program).
6-year residents typically spend 30-33 months on the OMFS service (sometimes the med school years include some OMFS rotations - be sure to include these when looking at programs). A friend of mine in a six-year program had the following schedule:
Intern Year: 12 Months OMFS
MS3: 12 Months Medical School
MS4: 8 Months Medical School, 4 Months of Anesthesia at Resident Level
General Surgery: 12 Months, split between Cardiac, Trauma and Plastics
Junior Resident Year (12 Months): 9 Months OMFS, 3 Months ENT
Senior Resident Year (12 Months): 12 Months OMFS
Total OMFS Time: 33 months OMFS
So, as you can see, there is little difference between the total time on OMFS between these two types of programs (granted that there are some 4-year programs that may spend much more time on OMFS than some 6-year programs, but the difference is only a few months for most programs).
As far as scope of practice is concerned, AAOMS maintains that there is absolutely no difference in the scope of practice between 4-year and 6-year guys. There have been studies that have shown that 6-year guys tend to have a wider scope of practice, but the authors of the study went out of their way to point out that the difference is NOT related to 4-year guys being denied privileges, but rather that 6-year guys are more likely to seek out privileges to do expanded scope procedures. However, no matter what type of program you go to, always remember that YOU ARE A DENTIST FIRST (AND A PHYSICIAN SECOND - if 6-yr).
Having spoken to numerous residents and faculty (both 4- and 6-year), there is some consensus that, regardless of what AAOMS says, there is a perceived difference in the public/medical community between single/dual-degree guys. Most people I've talked to attribute this to the fact that AAOMS hasn't done a good job educating the public about OMFS and what OMFS are trained to do. Let me be very clear - I'm not claiming that there is a difference between 4- vs. 6-year trained surgeons, but that some people, through their own ignorance, think there is and that the professional organization has not been effective at dispelling these ignorant beliefs.
My personal opinion is that you should do a 6-year program if you have the time and energy. I think that having the MD may also open up more options to you outside mainstream OMFS (head/neck oncology, cosmetics, craniofacial), but even in these areas you'll still have to constantly prove your worth to related specialists (ENT, Plastics, G. Surg). Also, if you intend on pursuing an academic career, an MD can be valuable in the hospital setting.