OpenRocket – open source simulation tool: http://openrocket.info/
RockSim – commercially supported software, not free: https://www.apogeerockets.com/
RASAero II – free, a must for supersonic flight: http://www.rasaero.com/
FinSim – free for non-commercial use. You have to email a request for the download link: http://aerorocket.com/finsim.html
BurnSim – for modeling rocket motors, not free and subject to export restrictions: http://www.burnsim.com/