Most behavior problems occur because the rabbit thinks its in charge. As the owner, we need to assert our dominance and let the bunny know that WE are "top rabbit". Once the rabbit knows that, it will think again about acting out or being bad. My pet rabbit, Elsie, used to be a nipper. She would nip (sometimes really hard), when she wanted attention or if she felt I was ignoring her. Needless to say, she's very spoiled:). But that doesn't mean that I can't train her AND keep her spoiled!
The next time she nipped me, I gently but firmly held her head down on the floor. She really didn't like it, but only five - seven seconds later she was back playing happily. Make sure you don't let the rabbit go when it struggles. That doesn't do anything. The rabbit just realizes - again - that it gets what it wants.
It only took a couple more times of her nipping me and me holding down her head for her to realize that, oh - when I nip Mommy something I don't like happens.
Every now and then she'll nip me again but I reinforce the same punishment. She hasn't done it in quite a while now. But, since I've said that, I'm sure that when I let her out to play later tonight she'll nip me. Oh well. As long as she knows I'M in charge . . . .
Not every "bad behavior" can be treated this way. This method can only really be used when the rabbit is causing you pain. But if the rabbit is peeing everywhere or chewing everything up, you'll have to use a different method.
For chewing, or anything similar, the best way is to remove and distract. If the thing the rabbit is chewing can't be removed from the play area (like carpet), remove the bunny from that area. Then, distract it with something else that the rabbit can nibble (such as a toilet paper tube or pine cone).
With rabbits who are peeing everywhere or "marking" their territory (or anything similar), just put an end to playtime. Shut the bunny up for a few minutes as a "time out", and soon enough it'll realize that when it doesn't pee in its litter box, it gets a consequence. Remember, though, that for bucks who are obsessive about "marking" their territory with urine, usually having them neutered completely eliminates this behavior.