How much spare space do you have on the OSX system HDD or partition? That is important. The problem is generally Java. But then, your problem sounds like a general utilities run over might not do it harm. Repair permissions with Disk Utility after a safe boot. And then use the repair from Disk Utility on the install disk.

Also consider Tip: Purge the Downloads Queue! as this can add a lot to Virtual Memory (VM) use. Reduction in incompletes will reduce HDD space used via VM.