The major difference between these tools is how they copy files.
scp
basically reads the source file and writes it to the destination. It performs a plain linear copy, locally, or over a network.
rsync
also copies files locally or over a network. But it employs a special delta transfer algorithm and a few optimizations to make the operation a lot faster. Consider the call.
rsync A host:B
rsync
will check files sizes and modification timestamps of both A and B, and skip any further processing if they match.
If the destination file B already exists, the delta transfer algorithm will make sure only differences between A and B are sent over the wire.
rsync
will write data to a temporary file T, and then replace the destination file B with T to make the update look "atomic" to processes that might be using B.
Another difference between them concerns invocation. rsync
has a plethora of command line options, allowing the user to fine tune its behavior. It supports complex filter rules, runs in batch mode, daemon mode, etc. scp
has only a few switches.
In summary, use scp
for your day to day tasks. Commands that you type once in a while on your interactive shell. It's simpler to use, and in those cases rsync
optimizations won't help much.
For recurring tasks, like cron
jobs, use rsync
. As mentioned, on multiple invocations it will take advantage of data already transferred, performing very quickly and saving on resources. It is an excellent tool to keep two directories synchronized over a network.
Also, when dealing with large files, use rsync
with the -P
option. If the transfer is interrupted, you can resume it where it stopped by reissuing the command. See Sid Kshatriya's answer.