http://ask.metafilter.com/57840/What-kind-of-network-cable-t...
Ground loops shouldn't be a problem as the APs have transformers that don't use ground at all so there's no ground connection to mess things up.
If lightning is a big issue you might need surge protectors on the lines. Is a Cat6 cable inside a plastic conduit that susceptible to getting hit by lightning though?
IANAE (electrician), but per my understanding, putting copper cable inside a PVC (or other plastic) conduit is among the worst things you can do; it gives the strike only one place to go: down the copper.
EDIT: I found a comment on a CCTV forum site that corroborates this: http://www.cctvforum.com/viewtopic.php?p=79496&sid=0e2686464...
This also goes for ethernet between buildings. Surprisingly enough if the building is poorly grounded the best path can be over your ethernet to a different building.
The ethernet transformers don't really help. They are just another part to get melted off the circuit board if there's a close lightning strike.
Surge protectors pretty much exist as a sacrifice to protect your more expensive electronics (switches and routers).
But yeah I helped on the Montreal meshnet and I think we either have or really want to have a RONJA link, because it's cool as hell as well as very useful in general.
This is not my area of expertise by far, so I'd love to know what I'm missing.