Risk management software packages (such as Risk+ and @Risk) are useful for quantitative risk analysis.
Decision support software (examples are Crystal Ball and Expert Choice) can be very effective for decision making in complex project situations.
Issue tracking systems, either purchased or based on a spreadsheet or other database, may be needed for effective integrated change management on large programs.
Time and resource tracking software can support detailed reporting requirements for government and some commercial projects. They can also support collection of earned value management metrics.