Rather than slowly transition, I decided to just switch over to Vibrams completely (this was Phil's advice and I had injured my shoulder, so couldn't do too much mileage anyway). That was about 6 weeks ago and I'm now at the point where I can comfortably go up to 7-8 miles, either on trails or road, and I feel like I have a long enough baseline to report back.
It wasn't that hard for me to transition. I started with really short, with a mile or so, and then worked my way up over the course of a month or so. If you're a foot striker you need to completely alter your stride so you land either mid or forefoot (this is pretty much the point of going barefoot). I started out mostly on asphalt, which you would think would be pretty hard without any cushioning, but it really forces you to concentrate on your stride: one or two (incredibly unpleasant) heel landings on asphalt with no cushioning teaches you real fast to adjust your stride. Anyway, once your stride adjusts and you learn to land softly, I at least didn't find that there was much trauma to my foot. At around week 3 or 4, I started to get some pain in the metatarsals of my right foot, but that mostly went away after a few more weeks.
Instead of the foot, the primary adjustment was in the calf. Because you land on the forefoot, and seem to push off more by extending your foot, it seems like you put a lot more stress on your gastrocnemius. For the first month or so my calf and achilles tendon would be sore after each run, and at least once I had my right calf completely lock up and I was limping for a few days. This has mostly gone away by now, however, and I feel pretty comfortable up to reasonable distances.
Surface and Terrain
I've now run in VFFs on a whole bunch of different surfaces. Dirt trails are the best, then grass, then asphalt, and then gravel. Basically this is an issue of cushioning: with VFFs you're much more sensitive to how hard the surface is and grass and dirt are just nicely comfortable and springy. (Note: I prefer dirt even with a real shoe). Asphalt gives you a harder landing and so is less comfortable, but basically fine as long as you are actually landing OK. The problem with gravel is that as the size of the rocks starts to get bigger you start to have to really watch your landing: coming down hard on a sharp rock the size of a golf ball can be quite painful.
Climbing hills is good: you would naturally tend to land on the ball of your foot anyway, so it doesn't require much of an adjustment in your stride. By contrast, going down is bad because you would naturally tend to heel strike so you need to really overcompensate to avoid that. And of course since you tend to strike relatively hard going downhill anyway, this is doubly bad. Even now I tend to come down harder than I would like.
The biggest problem with running in VFFs as opposed to shoes isn't the routine pounding but rather pebbles, rocks, acorns, etc. The soles are just too thin and flexible to protect you from this kind of impact. You can't always avoid stepping on rocks, but when you're running on a basically flat surface you can mostly see them in advance and when you do accidentally step on one, you usually notice before you've put your full weight on it and can just pull your foot back before you've done any real damage. I've only really managed to hurt myself twice: a week ago when I stepped on a small pinecone but landed on the side of my foot rather than the ball and wasn't able to correct. Then yesterday I want running on the baylands trail and there were just so many rocks that I couldn't avoid all of them and so landed pretty hard on a few.
Even in those two cases, I didn't do any permanent damage, just hurt a lot immediately and then ached for the next 5-10 minutes. It feels fine now, though and I don't see any bruising.
People often ask me about running with shoes with so little support: I have incredibly flat feet and I've never really found that having a lot of support did much for me; I find it more comfortable to just let my feet pronate completely the way they want to, even in normal running shoes. I don't know what VFFs would be like for someone with normal arches.
While I wear socks with regular shoes, I don't wear them with VFFs (you can wear Injinjis), and this hasn't been a problem for me. I have one friend who tends to get a lot of blisters with VFFs, but this hasn't been a problem for me at all (and I have gotten blisters with other shoes, so it's not like my feet are especially tough). I suspect this is primarily an issue of fit. For longer runs, it seems like I might be getting a few hotspots and I've been trying to slather on some Hydropel as a precaution.
You need to be a bit careful about stubbing your toe. There's not much protection and if you scrape the top of your toe, you can tear through the thin nylon at the top or peel the rubber sole away. I've got a small tear above my big toe. So far it's not expanding but I've ordered a new pair just in case.
I suspect I'd be able to run much longer in VFFs (and I'll try a 10 this weekend), but given how much trouble I had when I ran on grave of the wrong size, I'm not sure I would want to do something like an ultra, where I couldn't turn around and didn't know that the surface would be good. In view of that, I'll probably start mixing it up more to make sure I still can run in shoes if I want to.