NEVER pick a rabbit up by his ears. This is extremely painful for the rabbit and is very cruel!!
When you go to pick up your rabbit, support his butt with one hand, while scooping him up directly behind his front legs with your free hand. If he wiggles too much for you to do this without dropping him, gently but firmly grasp the skin behind his ears on his neck and support his butt/back legs with your other hand, and scoop him up this way. If done correctly, this method will NOT harm the rabbit in anyway.
Here are photos to help you out:
**coming soon**
You can also "hypnotize" your rabbit to make routine grooming sessions such as nail clipping and checking the teeth much easier and less stressful for you both. To put your bunny in a trance, cradle him on his back and firmly but gently stroke his nose. He should begin to seem to calm down a bit. With some rabbits, they seem to almost fall asleep and go limp as a ragdoll when they're in a trance!
And always remember to be quiet and avoid many sudden movements around your rabbit. They'll respond to you much better if you approach them in a non-threatening manner.