I don't think it is a disease personally.
I don't know of any disease or parasite that can kill both fish and inverts.
IME typically inverts are fairly resilent to disease.
I think it must be something with the conditions of the tank
perhaps a contamination?
are your corals doing okay? what kind of corals do you have?
did you add any rock recently and did you test for copper if you did.
LR can hold copper and it will leech slowly back into your system.
I would definitely add carbon to see if you can contain any contaminents.
although the copper wouldn't affect the fish, it would definitely kill your inverts..and alot of other things such as bristle worms, amipods etc...
do you still see the critters swimming around your tank when the lights are off? see bristle worms when you feed? or any snails or crabs still alive?
if not, then I would definitely suspect copper...(although if your corals are doing fine..probably not copper either)
this die off could certainly cause the conditions of your tank to go south..which in turn would make your fish more prone to disease that they had previously been able to fight off.
however, diseases aren't something that linger around in your tank without being noticed...most diseases will either become noticeable or not.
so if you haven't noticed any disease symptoms within the last 3 months, not really sure what could be killing beyond something in your tank.

I'm trying to think back to see if there were any new dosing etc. around that time, but nothing comes to mind. I started dosing kalk in Oct 2011, but that was way before this all started.

I've often wondered if I've got a copper problem in the system somehow. I've always struggled to keep snails, and while I did have a healthy population of pods for the first half of the tank's life, it's been greately reduced lately. I've tested for copper multiple times, and even went so far as to run some cuprisorb in a reactor for an extended period of time, but there was no color change whatsoever. Last copper test was Nov 2011. Will test again just for fun.

I've got a mixed reef, some easy SPS (birdsnest, red digi, green monti cap that's never been green, bird of paradise), couple LPS, branching hammer & trumpet, a big GSP colony. Certain SPS I've struggled with, pretty much anything except what I've got now so I've given up on it for the moment. Tried some green stag, yellow digi etc. but no success. The LPS has always grown quickly, but for the past year I've found it does not expand nearly as much as it used to, which is a shame as LPS is probably my favorite. I'd love to pick up a nice torch but I'm not going to bother until my current colonies start expanding like they used to.

I usually do run carbon in a reactor. Got a little lazy with changing it lately, but it does get refreshed maybe once every month or two.

I appreciate all the feedback and discussion, I would love to get to the bottom of this. While I'm somewhat green in terms of experience (only been reefing for about 2-1/2 yrs), I'd like to think of myself as being pretty well read and it's frustrating to struggle with simple things while I see others making huge mistakes and keeping all sorts of corals etc. that I've never been able to. Now to think that I can't even keep fish and hardy inverts, not very good. Thanks again.

Just did a copper test on the new system, I thought I saw a reaction (color change) at the beginning of the test but giving the test time to develop yielded no measurable result. Nonetheless I've done some reading on copper and heavy metal poisoning and I think I'll go pick up a poly filter to run just as a preventative measure. The symptoms sure seem to fit.

Also, I discovered that I was breaking a bunch of rules of copper; wasn't waiting for kalk mixture to settle before allowing ATO to pump it into the system, and was not considering copper sneaking in with alk and calc additive dosing (was only concerned with preventing large chemistry swings).

What your skimmer leeching micro bubbles into the tank? Our tank at work was doing that and almost everything died, well that and the combination of ich. Also do you have any toxic inverts/fish that could release toxin into the tank? such things could cause a whole tank crash.

Not sure how to answer the microbubbles question. When the ATO resevoir would emptly (and I didn't notice) and the return chamber got to a certain point then yes the return pump would shoot micro bubbles into the system. I wouldn't call that an ongoing problem though. I beleive the loc-line return pipes did leach a little bit of air into the system and blow a very small amount of micro bubbles into the system too, but pretty minimal and no more than were present back when the system was stable.

Currently I do have a micro bubble problem on ver 2.0 of the system, but I have a few things yet to do to resolve that issue.

As for toxins, I don't think there was anything exotic in terms of livestock that would emit toxins while alive, but perhaps after death? There are a few zoa & paly colonies in the tank which we know are toxic if damaged, but no major trauma to those. On the list of inverts that died and decomposed in the tank include a large pincushion urchin, smaller tuxedo urchin, two small red starfish, brittle star, numerous snails and hermit crabs. There were only four fish listed in previous posts.

Dosing is pretty minimal; IO salt, BRS Kalk (not using anymore), occasional Seachem Calcium and Reef Builder Alk supplements. Was experimenting with dosing iron and Lugol's a while back, but it had been quite a while since the last dose of those.

I personally don't see how micro bubbles would kill anything

Don't quote me on this cause I'm no expert but I believe the micro bubbles can get trapped in the fish gills and cause respiratory problems, there's a disease called bubble disease in fish. Also if the micro bubbles comes from the protein skimmer the bubbles carries the protein trapped on the bubbles and when it gets built up it could cause problems.

Xadieu, I didn't mean to sound rude..sorry if it came across that way
I have microbubbles from my skimmers entering into my systems from all my systems...so I don't know how prone fish would be developing problems.
I think it would have to be very extreme to be problematic.
as well, it doesn't really explain the invert die-off.

Hehe no worries I was not offended by it. But I cannot explain how the invert dies except for copper level and rapid change in salinity.

New development
 

So it would seem that whatever was affecting the livestock is still present. Last night I picked up two cleaner shrimp that were to provide some life in the tank for the next 2-3 months. This morning I found them both dead, pretty much un-moved since they were introduced to the tank last night.

Now either something went very wrong during acclimation, or there's some kind of mystery death in my system which I can't pinpoint. I've acclimated many an invert before, always succesfull. I'll go over things from this time though, maybe something will stand out:

Shrimp spent about 1/2 hour in the bag on the way home from the LFS, mix of sitting on the seat and in my lap to maintain temp.

Got them home and into a bucket with a thermometer, started a slow drip from the DT. When they went into the bucket, their water temp was 74 something. Using my standard method of warming the bit of water (glass full of warm water placed into the existing water), I slowly brought the temp back up to about 78 deg.

Two hours later, temp sitting steady at 78, time to go into the tank (which was at about 80deg.). Scooped up one shrimp and gently into the tank, where it clung onto my fingers for quite a while. Finally convinced it to let go when it sank (not swam) down to the bottom. Same thing for the 2nd one. They looked stunned, the odd cleaning of antennae, but no big movements.

There they stayed overnight, this morning, and now at lunchtime I happend to be home and checked them again, at which point they were both dead.

Now I'm really getting puzzled with this whole thing, it's like there's some mystery poison in the tank that's killed ALL of my fish and inverts, and putting a hurt on my corals. My LPS open up to feed at night, but have absolutely no extension during the day. All are completely deflated.

Ran a few measurements again last night, SG was down a little (1.024) so I slowly added the necessary salt to bring it back up. Alk was still down (6.7)despite my last dose a few weeks back, so I added 1/3 of the necessary dose to bring that back up as well. Other than that, no ammonia, no excessive nutrients (very little algae groth), skimmer's long settled down after the move. Running carbon in a TLF 150 reactor, and a poly filter. Baffled....