Compare two folders even excluding particular files or subfolders, with NewDirDiff
NDD (=New-Dir-Diff) is a free utility that will help you check if two folders are the same; it checks for files and subfolders and displays graphically all differences.
NDD is the replacement of EZ folderFx, a similar tool that suffered many limitations.
Features: exclude list for files, extensions and folders; history of the last compared paths; entire disks can be compared; folders can be passed through command line.
The program is not in active development and it may face problems completing a task.