This week's giveaway is in the EJB and other Java EE Technologies forum. We're giving away four copies of EJB 3 in Action and have Debu Panda, Reza Rahman, Ryan Cuprak, and Michael Remijan on-line! See this thread for details.
The only option that I know of is to select Run->Run... to open the runtime configuration dialog. In the Configurations list, select each run configuration that you want to remove from history and click the delete button below the list to remove it.
"Write beautiful code; then profile that beautiful code and make little bits of it uglier but faster." --The JavaPerformanceTuning.com team, Newsletter 039.