Maybe he was thinking of midi-chlorians? Those are totally legit when they show up in a peer-reviewed journal.

The word mitochondria is just a personal flag, a smell, that I use as part of a warning.

Mitochondria raise flags because of people like the UK Dr Ruth Myhill. She claims to be a researcher on chronic fatigue syndrome. CFS is real, but sadly is an area rife with cranks. Myhill appears to have a lot of crank-like beliefs. Her "research" is hopeless, and amounts to unlicensed unethical experimentation on desperate people.

I guess, although I have no supporting evidence, that the word mitochondria is used more often by cranks than other organelles.

Mitochondria are pretty important (as is most of the junk in our cells for that matter). I'd be less wary of the use of mitochondria in popular science - it's shorthand for talking about the energy metabolism pathway, and doesn't indicate one way or another whether we're looking in the right spot for the causes for particular diseases / syndromes.

On a tangential note, I haven't read it, but http://www.ncbi.nlm.nih.gov/pubmed/21792218 might be an interesting review on CFS. Also, I assume you are referring to Sarah Myhill rather than her daughter.

Cellular organs are a pretty untouchable class of things for anything humans are going to do on a macro-scale. If you're proposing to achieve a big effect from say, a diet, then focusing on more then 1 bodily component is suspicious because there's a huge range of barriers you need to get through to get to it (without damaging, generally).

There are lots of drugs, for example, which are useless because although they target the right protein and have the desired effect they can't actually get to it via normal metabolism and the like.