How can I best copy large numbers of small files over scp?

You can pipe tar across an ssh session:

$ tar czf - <files> | ssh user@host "cd /wherever && tar xvzf -"

Tar with bzip2 compression should take as much load off the network and on the cpu.

$ tar -C /path/to/src/dir -jcf - ./ | ssh user@server 'tar -C /path/to/dest/dir -jxf -'

Not using -v because screen output might slow down the process. But if you want a verbose output use it on the local side of tar (-jcvf), not on the remote part.

If you repeatedly copy over the same destination path, like updating a backup copy, your best choice is rsync with compression.

$ rsync -az -e ssh /path/to/src/dir/ user@server:/path/to/dest/dir/

Notice that both src and dest paths end with a /. Again, not using -v and -P flags on purpose, add them if you need verbose output.

use rsync, it uses SSH.

Usage:

rsync -aPz /source/path destination.server:remote/path

The rsync switches care about compression and I-Node information. -P displays progress of every file.

You can use scp -C, which enables compression, but if possible, use rsync.