Application/Network Performance

I a network manager for a large company, I currently oversee a network of 2500+ devices. We currently have software that allows me to see packet transfer times that allows us to identify bottlenecks and problem users. I am looking for a little more detail though. Our routers are mainly Cisco, is there anything out there (software or appliance) that will collect NetFlow data for me to further analyze?

Thank you,

Jason