Copying with excluded files and directories on Windows
xcopy /S /E source destination /EXCLUDE:ExcludeFile.txt
Copying with excluded files and directories on Linux, Mac OS X, or *nix
tar works well for the task at hand
tar -X exclude_file.txt -cvf - source | tar xvf - -C dest
rsync also has exclusion functionality built in:
rsync -r -t -v -b /source_folder /destination_folder
with additional args--exclude 'bad_directory'
(the exclude.txt file)path/to/BIGdir monkies.*
And cp with find, the superuser source of some of these commands. I didn't spend too much time with the last one but it was hiccuping on OS X with directory copying.
find ./source -not \( -name exclude_1 exclude 2 \) -print0 | xargs -0 -IFILES cp FILES ./destination
I tried a variant of this command and while it copied directories, it also copied their contents into the top directory at the destination destination.
find ./source -mindepth 1 -not \( -name exclude_1 exclude_2 -prune \) | xargs -Iitem cp -r item destination