Seems like a lot of people have this same problem. Including me.
I have a 55 gallon reef and I had 2 firefish, a blue-striped goby, and a royal gramma disappear on me. Plus countless peppermint shrimp. I didn't really worry about it too much, since my mom lets her dog run around untended and I've had a few jumpers before (which I found before the dog). But recently with the mysterious disappearance of my beloved full 5" Blue Tang, my large Skunk Cleaner, and a large emerald crab, I'm getting suspicious. I also had a Coral Beauty that was fine one day and died the next, but unlike the others, I found the body untouched. I'm breaking down my tank this week for an upgrade, and hopefully find out what's behind it all.
Something I'd like to point out, though. All of the fish and inverts that I mentioned had a tendency to sleep hidden away in some crevice and often during the day as well. My tang, skunk cleaner, and crab were on and off behind the rocks, in front of the rocks, which might explain why they haven't been touched until recently. I have a clown that I've had since day one that's always out in the open and is still with me and a medium-sized algae blenny that does the same.
However, I've stayed up late with a red flashlight to see what I could find. I've seen a bristle worm, which I think might account for the shrimp, but for a large blue tang? I also saw some sort of brown worm, but only it's head. It looked pretty much like an earthworm and recoiled really quickly when I hit it with the light. I've read about a huge one taking out lots of coral, but a small one in a 55 taking out full-sized fish?