We all seem to be supplementing with magnesium (in probably a low-phytate intestinal environment), which is necessary for optimal mitochondrial function, so we're all pretty much set there.
I think manganese deficiency is possible with a paleo diet, especially for those eating VLC or ZC. Manganese superoxide dismutase mitigates mitochondrial ROS production.
100g of raspberries actually has more manganese than 100g of liver, which has quite a lot more manganese than a steak. If you're avoiding berries and other fruit, it's probably wise to get manganese from bivalves of some sort or to find a bioavailable supplement like manganese picolinate. I think it's safe to assume that the food supply is far more deficient in manganese than what would be encountered by a human in the wild. The bioavailability of manganese from high-phytate nuts is questionable as well.
The entry of fatty acids into the mitochondria is rate-limited primarily by CPT1, which is an enzyme that transfers partially oxidized fatty acids toward the mitochondrial matrix. It requires carnitine to do this, which just about all of us should be manufacturing sufficient quantities of given our (presumably) high-meat (and thus high lysine/methionine) diets.
Anyway, are there any other nutrients we should be ensuring that we consume in adequate amounts so that our mitochondria are humming along?
Edit: http://www.sciencedirect.com/science/article/pii/S0098299705000415 Looks like adequate iron and zinc (no, really) are needed for optimal mitochondrial function as well as biotin and B5.
Edit 2: http://www.marksdailyapple.com/managing-your-mitochondria-nutrients-and-supplements/ MDA has a post today about this subject that seems to pretty much be in line with what's been said.
PQQ, Mg, Carnosine, Alpha lipoic acid, pyridoxal 5'- Phosphate, resveratrol, Ubiquinol, L-carnitine, and high dose vitamin C.
PQQ is the top dog to me. Take a look at this link and see how much more powerful it is compared to Vitamin C.
Rucker R, Chowanadisai W, Nakano M. Potential physiological importance of pyrroloquinoline quinone. Altern Med Rev. 2009 Sep;14(3):268-77.
Lipoic acid is excellent for mitochondria. It's often called the "universal antioxidant" because, unlike other antioxidants, it scavenges both water and fat-soluble free radicals. Food sources are your first line of defense, but you may want to consider supplementing with R-Alpha Lipoic & Acid Acetyl L-Carnitine.
Weight training and cardiovascular exercise are both great for generating mitochondria. There's a vast amount of quality research showing this. Google. All else being equal (nothing ever is, but I like the phrase), athletes with the most healthy/efficient mitochondria come up with the best performances in endurance events. Obviously this holds for the endurance contest called Life. The longer we can extend the lifespan and advance the health of mitochondria, the longer we live. Not a magic bullet; there are many factors to healthy longevity, but still...
Coenzime Q10 is most important: http://faculty.washington.edu/ely/turnover.html
Piracetam is shown to boost mitos. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1615864/ http://www.frontiersin.org/neuropharmacology/10.3389/fnins.2010.00044/full
Ketogenic diet http://www.ncbi.nlm.nih.gov/pubmed/18466343
(R)-α-Lipoic acid, a mitochondrial coenzyme http://www.lef.org/magazine/mag2011/aug2011_Lipoic-Acid-Reverses-Mitochondrial-Decay_01.htm
How efficient are your mitochondria? 6 Answers