We have developed PPrate, a passive capacity estimation tool that from packet traces (such as tcpdump files) obtains a reported accurate narrow link capacity of a certain flow, it can be even used inside TCP. The tool is based on pathrate algorithm and applies a number of techniques to overcome limitation of TCP layer and applications layer on the dispersion measurements.
For more information about how PPrate works, you can read the following paper: PPrate : A Passive Capacity Estimation Tool.