bad dreams?

This doesn't happen to the dogs I have now, but I have had dogs who did that. It's usually combined with a lot of body twitches, which indicate REM sleep. I used to just gently put my hand on the dog and stroke him a little bit. He wouldn't usually wake all the way up, but it seemed reassuring, at least to me. I would try not to overreact and shake him or holler.

I think they are sometimes "trying to bark" and it comes out as wimpering instead of barking...they may not necessarily be having a bad dream. I would be careful about waking her up. If you wake humans up every time they are in REM sleep, it can causes health issues because REM sleep is thought to be needed for maintaining a variety normal bodily functions. Don't know if it's the same for dogs, but my guess would be that it is. Maybe try what Madeleine suggestion by just stroking her...but not actually waking her up.

It is similar to humans sleepwalking or talking in their sleep. In her dream she is probably running, barking or doing whatever. During dreams, the brain is actively acting out these thoughts. The brain is supposed to tell the body that these are just dreams and to not act on them. Sometimes, the body gets incorrect transmissions from the brain during sleep that it shouldn't and the body reacts - but not fully. Therefore, a bark or howl may sound like a whine or cry to you. They are not in pain or anything...just dreaming like the humans do. I don't mean to come across as fully educated on the subject. This is just what my Grandpa, who is a doctor, tells me.
I do it all the time and Mama just lets it go unless it is interrupting her sleep.

My dogs do this too sometimes. The other day Minnie was laying on my lap while I was watching TV. She started twitching and whimpering and actually let out a small bark! It surprised me because they don't normally bark while dreaming. I do the same thing as Madeleine's mom. I just pet them. I have woke Beverly once or twice because she was shaking all over and actually crying out, not just a whimper. It was so pitiful, like someone was hurting her. I couldn't stand it, so I gently woke her. She seemed a little shaken, so it could have been a bad dream. I don't know what happened to Bev before I found her, but I think she may have been treated badly.