Are you using a CP (i.e. cPanel, DA, Plesk, etc) or a barebones system?
If you're using a CP, it'll most likely be faster and less hassle to perform the migrations using the GUI. If you're using a barebones system, RSYNC or SCP works well. Ideally you'd want to dump your databases using mysqldump and then restore them on the new server, though if you do a mysqldump beforehand, you can use RSYNC or SCP to copy over the databases with the files.
Alternatively, if they're relatively small sites, you could simply GZIP the directories, copy the file over to the new server, decompress and then move the databases over. It really depends on the size of the sites.
There are also quite a few plugins that can aid in moving your WordPress sites from one server to the next. One that comes to mind instantly is BackWPup.