You could use the Robinson-Foulds metric. There are a few programs out there that calculate this metric. HashRF is one of them. You can also do it in Mesquite. You can also do it in R, the phytools blog shows you how. What you use will depend on what type of output you are looking for.
If you just need a metric, robinson-foulds will be fine. I have used the KTreedist program in the past, but there are many other out there.
I recently added the method to the ETE toolkit, so you can compare two trees in a programmatic way. The development version of ETE at github includes some nice improvements in this direction, mostly allowing to compare trees of different size, exclude branches depending on their support or the use of custom node attributes.
Note also that the ETE's robinson-foulds implementation will return the distance between the trees as well as the set of partitions in both topologies, so you could identify where the differences are.