how to compare two folders and copy the differences

It's not entirely clear to me what you want to do. The excellent, and free, TextWrangler:

http://www.barebones.com/products/textwrangler/

will compare folders and their contents. Use the 'Search > Find Differences...' menu item and select 'Compare: Folders' on the dialog that it opens. Lots of options, filtering, folder depth, etc. You get three lists: Only in A, Only in B and stuff in both A and B and can easily review differences and copy/move them around.

Wikipedia has a list of tools and features for comparing folders

http://en.wikipedia.org/wiki/Comparison_of_file_comparison_tools

If I've misunderstood and your aim is to synchronise two folders, e.g. for backup / archiving purposes, then the above won't help.

C.

I'd use a program like Sync-two-folders to do it.

Synkron