Unclassified exceptions can be fatal. The hard part is identifying the problem layer. Have you updated to Update 1 and added Update 1b? This really does improve stability and performance. Are there any other messages immediately prior to the unclassified?
My first guess might be problems with Raster layers. What formats for Raster images might you be using?
One way to try and diagnose the problem layer is to look at the Access.log and look at the entries just prior to the first unclassified error in the Error.log. The entries in the Acces log may include a reference to the Resource (layer or feature) being used just prior to the error. If you can identify the layer then try removing it from the map and see if the behavior changes.
If we can determine what the problem layer is we might be able to fix it.
We do have some issues under load with some raster formats, particularly under heavy load we have seen ECW (despite it's excellent peformance) cab cause some unclassified exceptions and cause a hang.
What is your server(s) configuration and basic specs (OS, # of cores and RAM) and how many users are concurrently using the system?
Dave