Use o WinMerge , um programa gratuito e fácil.
WinMerge is an Open Source differencing and merging tool for Windows. WinMerge can compare both folders and files, presenting differences in a visual text format that is easy to understand and handle.
Se você quiser algo mais poderoso, tente BeyondCompare . Não é grátis, mas tem um teste gratuito de 30 dias se você quiser testá-lo.
Beyond Compare allows you to quickly and easily compare your files and folders. By using simple, powerful commands you can focus on the differences you're interested in and ignore those you're not. You can then merge the changes, synchronize your files, and generate reports for your records.