Lion (10.7.2) -- CPU heats to 90-degrees and Java apps crash -- why?
For the CPU temperature to get those sorts of levels something needs to be hammering the processor pretty hard. I'd start by looking at Activity Monitor to spot which particular process has decided it wants a supercomputer cooling system.

If it turns out to be Java (which is likely), trash Java from your system and then reinstall it from there. It could be a damaged cache file, the application might have corrupt preferences, or some other combination.