Some of the best cave diving in the world is in Missery- if you like cold, dark, low vis caves.
There is Mine Lamotte- which is an old mine- I've never been there. You might find mention of it recently in the Accidents and Incidents forum. :11:
Roubidoux Springs in Waynesville has a decent sized cavern zone, although it's hard to enter at times because of the flow through the entrance which is approaching a restriction. I think the best vis I've seen in there was approaching 20'-25'. Beyond the cavern zone, the cave gets dark and deep quickly, so it's certainly not a place to be fooling around.
I've never been to Cannonball, but I hear this is a nice cave with a long walk up and down a hill and has an entrance that is hard to find and considered a restriction.
Bonne Terre Mine is more like a guided tour through a mining museum that happens to be in an underground lake. For most of the tours, you can surface directly into the air above, which happens to be underground. It's lit from above and, the last time I was there, the management didn't allow powerful lights. I think this was to prevent people from wandering off on their own. The water is quite clear- I'd like to say that you could toss a quarter, in a hyperbolic arc, off the dock and see if it lands heads or tails- 100' below. The water temp is about 55' degrees year round which makes it downright cozy in a 7mm in the middle of winter.
It's rumored that Bonne Terre connects to other mines in other towns, so in theory, you could swim from one town to the other, although I've heard this entails passing through tight restrictions at 300' (read: take all your gear off!)