I try everything else first rather than scruffing them. While I've never heard that it will suffocate them, picking a rabbit up by the scruff, especially a larger/adult one, separates the skin from the muscle beneath. 
Unlike cats, rabbits never pick up their babies by the scruff, and their bodies are not built to withstand it (and if anything would make them feel like a predator had them, it would be that!). I have seen the damage when butchering and don't want to have any part in that.
Only very rarely do I grab rabbits by the scruff, but sometimes you're not left much choice. (I like my rabbits, but I am not willing to sacrifice my own skin for them!) In those incorrigible cases, I collect both ears and scruff in my right hand, but I do NOT lift or carry a rabbit that way. Once their ears and shoulders are immobilized, they tend to stay still, though I would not call it relaxed. When I have them immobilized, I reach under them and lift them, by the body, with my left hand. Sometimes my hand is under their belly, sometimes it's cupped under their hindquarters - this depends on how big the rabbit is.
I don't carry them that way, either, since they tend to start flailing if you have very far to go. What I normally do is pull them up against my own body and carry them that way (my rabbits are gentle, even when they're being pills about being taken out of their cages). But I also handle a lot of other people's rabbits which are not gentle, and if I'm afraid a rabbit will bite me, I flip it over on its back in the cradle of my elbow and carry it that way. I've had nasty angry does furiously chewing on their own dewlap in that position, but they couldn't get to me. 
Once you get where you're going, you just roll the rabbit forward onto the table/ground/whatever.
If you're moving rabbits from one cage to the other, or out to a pen in the yard, and you have trouble keeping them in your arms for the trip, you might consider just bringing a small carrier or even a cardboard box to the cage, pulling the rabbit from its cage directly into the carrier, then carrying them in that. That's what I have smaller kids do with very large rabbits.
