rsync rocks. Here, we'll use it to 'synchronize' a remote folder with a local one, while excluding a couple files. rsync can even pick up where it left off if interrupted, and it won't overwrite data unnecessarily!
Here's the general form of local -> remote:
rsync -avh --exclude 'path/to/exclude' --exclude 'path/to/exclude2' /path/to/source user@server:/path/to/remote/dest-a for 'archive', which is rsync shorthand for "recursion" and "preserving almost everything", -v for verbose, -h for human readable numbers. --exclude excludes files from transfer and is relative to the source path!.
There are a million ways to use rsync, and lots of flags. A couple of others I've found useful include -P for showing progress, -z to enable compression, --delete which provides a powerful destructive updating ability, and --dry-run to safely test the command.