I agree with IPSLA and VNQM being good choices for measuring network performance quality, but only if you have Cisco devices. With IPSLA, you can measure the performance between your edge Cisco device and the remote location Cisco device.
In case you do not have IPSLA capable devices, you could also try using NetFlow / sFlow / J-Flow. Flow technologies can tell you the IP Addresses and applications using the bandwidth, what their destination is and the priority for each IP conversation. You can enable NetFlow on your edge device that connects to the remote site and check if you have enough bandwidth or maybe incorrect application priority. But this will require installing free or trial version of NetFlow Traffic Analyzer and adding your device to NPM.
R,
Don