Yes, bunnies do make noises!
When a bunny feels threatened or annoyed, you may here a growl. Growls tend to be fairly soft (even though your bunny is probably convinced that he or she is as loud and threatening as a lion). They often sound like 'HUFFF!' and may be accompanied by boxing or a lunge.
This video shows a cage-agressive bunny growling. You can hear it very well starting at 0:53. NOTE that this bunny owner takes care to include many notes about the video, which you can read on the youtube page for this video. From her description, it sounds like this bunny is actually well-cared-for and this video was taken to demonstrate this behavior.
Honking is often a sign of pleasure. Some bunnies honk when they are eating, getting treats, getting attention, or snuggling.
In this video, if you turn your volume waaaay up, you can hear a bunny happily honking as he enjoys some fresh veggies.
You never want to hear a bunny scream. A scream indicates severe pain or fear, and is a sign that your bunny needs help, and needs it fast.