If you have ever used Beyond Compare from Scooter software, I don't have to tell you this is a great directory/file comparison tool, especially for the price (Single licenses are listed at $30). If you don't use this tool, I highly recommend you take the time to download a copy and kick the tires for the 30 day trial. As I recall with version 2, the trial period lasted for 30 usage days, not 30 days from install. I don't know if the same applies for version 3.
The comparison is far better than the comparison that comes out of the box with Visual Studio 2005/2008 and/or Team Foundation Server. However to set it up you have to follow a few configuration steps. These are well documented by Marc Brooks at this entry (Beyond Compare 2), and in more detail by James Manning (Beyond Compare 2 & 3).