You traitor!

[thump] You weren't supposed to follow the little human and hop back in your cage for treats.  I was having fun!

There was a bit of end of playtime drama last night where River took the hint after I put all of their toys away and followed my hand signals to go back in her cage.  Simon had to be bunny-wrangled after his temper tantrum.

Access denied.

River once again tried to get behind the entertainment center.  This time, the Coke box and a 25 lb box of hay stood in her way.  She was so frustrated that her plans were thwarted that she thumped.

Genuine surprise to see me bunny wrangle her back into the living room.

What witchcraft allowed you to know I was there?!  I'll be watching you from now on.
Being deaf, I honestly don't think River realizes that thumping produces noise.

Bunny shaming.

Every once in a while, Simon tests the waters to see if thumping will get him attention.  This time, I obliged...just not in the way he expected me to.

Who knew this was a thing?

That tan piece of cloth with the bunny hork on it is part of an ingenious solution to help alleviate Simon's newly recognized separation anxiety.  Yeah, we didn't know it was a thing either until one evening I was preparing some food for the next night's dinner and was out of Simon's line of sight.  Within 10 minutes of me "not being there" he started to thump rather loudly and insistently (much like he does whenever I would go to bed at night).  It was then that I noticed the pattern of timing and this only ever happening at night after the sun had gone down...

I asked my husband to do a quick Google search for rabbit separation anxiety (so I could still be out of his line of sight) and darned if there weren't similar stories from other people.
As an aside, you can see the foam furniture padding we placed under his cage to help damp the noise a bit (along with their kitten brush and the ridiculous amount of fur they produce during a heavy shed in the baggie--hey, it keeps it from going everywhere and gets tossed when it's full).

We found some tips and tricks to help lessen this all night random thumping that has been going on since November.  Here's the link to my original post:  http://bunnies-and-sunshine.blogspot.com/2012/11/no-simon-thats-bad-simon.html
Quite honestly, we were at the end of our rope at this point and I had no problem giving the little fuzzball the shirt off of my back if it would help solve the problem (I had only gotten a few hours of sleep per night for over a week, so the 2 hours of interrupted sleep the night prior due to the thumping had me wanting to cry I was so frustrated with him). 
It was clear that he wasn't afraid of anything or in pain, just that he wanted (or needed)  my attention.  We were both so tired of the thumping that our gallows humor kicked in and resulted in giving Simon the motto:  "When in doubt, thump it out!" 
What you see Simon playing with is a tee shirt that has my scent on it (I literally gave him the shirt off of my back that evening).  He never chews holes in it like the other cloth pieces in his cage, just nibbles it to shape it and gets bunny hork all over it before snuggling with it like a security blanket.

The combination of the shirt and ignoring the thumping (not giving him positive reinforcement for that behavior) has really helped decrease the night time thumping.
I'll be honest, the first night made us wonder if this was doing anything at all (I think it got worse because he realized we were ignoring him), but over the next few days, the frequency and duration of the thumping started to decrease and after about a week, we only noticed him thumping in the morning when someone's alarm went off/a light turned on so he knew one of us was awake (and he tried to demand early pellets from us).  This has gone on for a couple of months now, so I really think this combination of tactics is working for us.
We're still working on stopping him from making the morning noise, but it's happening less often now and we've managed a few nights strung together of no thumping at all, so that's a start.  The only time we find his behavior getting a bit worse is when we have visitors or there's some change to the normal routine, but it reverts back to normal within a few days.
Uninterrupted sleep is awesome!

No Simon, that's a bad Simon!

This is Simon (aka: Mr. Thumpy Clumperson) sulking after being repeatedly scolded for thumping every hour on the hour the night before.
Initially, I thought it was River making the noise because she's thumped before while having a nightmare and being deaf, didn't wake herself up.  To my sleep-deprived surprise, as soon as I checked River's cage, Simon decided to have an all-out conniption fit of loud thumping because I was ignoring him.  I rushed over to his cage to calm him down before he woke everyone within earshot.
I tried to scold him after realizing that he was doing this for attention by scooping up his front paws to ensure he was paying attention to me...he proceeded to happily lick my hand like an attention-starved puppy.
It was a long night because I had to stop him each time he started thumping by picking him up and saying, "NO thump, Simon."  Keep the command simple...bunnies seldom care about proper grammar (and at 4am, I didn't either).
Simon is lop flopping on my first attempt to sound proof his cage.  Turns out that it's pretty comfy.

Sadly, I think he took getting his own towel as encouragement.
Night 2 didn't play out much better.  More attention thumping (about 3 rounds worth of it).
I had decided to try a different tack--lay out the gray towel under his cage to help muffle the sound and not give him the attention he was seeking.  When he realized he wasn't being heard (we were ignoring him), he became louder.  Not cool.
I had to go out to stop him, but this time I got down on his level, blew a huff of air at his fur to get his attention (all the lights were off), then proceeded to turn my back on him and sit down for a count of 10, then walk away from him without acknowledging his presence.
Success!
This is bunny-speak for, "You really screwed up and I'm mad at you."  The fact that I didn't look at him afterwards told him he wasn't forgiven for his transgression.  At least the episodes of thumping were less than the night before.  Progress is good!

Day 3 I decided to get creative and if you look closely, you'll see that on top of the gray towel there is a slate colored pillow case just under the bottom of Simon's cage.  I decided to place about 12 layers of cut-up tee-shirts, sweatshirts, felt and that rubber cupboard liner stuff to damp the sound.
To hedge my bets after tapping the bottom of his cage and still noticing a good amount of sound, I placed shredded paper bedding under his hand towel to pad the bottom of his cage.
Poor River is confused why Simon is getting fussed over and wonders how come she can't have cool stuff in and under her cage too.  Short answer, she'd starve herself by hiding her food and never finding it again once it got mixed in with the bedding--she is quite the digger.

Night 3 I discovered that if you build a better bunny sound-proofing system, the bunny just cranks the volume up to 11.
Here is Simon at 2:53am having achieved his primary objective of waking the little human up.  It's like he's saying, "Oh, hi!  Well, since you're up, wanna play with some of my toys?  The cream cheese box is really fun to stick your head in and toss about--I even hang it off the side of my cage!"
I snapped the pic, then did the whole back-turn 'I'm ignoring you' thing.
Success!  That was the only time he thumped that night!
Hopefully this will be the last of it and I will have broken him of this bad habit.  Only time will tell.
UPDATE:  We think we figured out the problem--bunny separation anxiety.  Here's the link to my post http://bunnies-and-sunshine.blogspot.com/2013/07/who-knew-this-was-thing.html hope this helps!