Not all FTP programs have moved into the 21st century to support secure FTP protocol, but the vast majority have.
Here are some programs which we've tested that support encrypted FTP connections -- all of them being FTP clients of some kind.
Free SCP, SFTP and FTP client that can perform typical file transfer operations securely and fast.
WinSCP can connect to sFTP servers, backup to FTP and edit PHP files.
Fully-featured and free FTP client with Site Manager supporting secure connections, SFTP, SSH and a dual-panel interface for fast and reliable file...
FileZilla can connect to sFTP servers, edit PHP files and edit HTML documents.
A powerful FTP client supporting secure connections and the possibility of site-to-site transfers with an Explorer-like interface with many functions.
Core FTP LE can connect to sFTP servers, edit PHP files and edit HTML documents.
Fast and commercial FTP client application which supports all of the common standards, sporting a clean and intuitive user inteface.
WS-FTP Pro can connect to sFTP servers, backup to FTP and edit PHP files.
Powerful FTP and FXP client which can transfer files in high speed with site-to-site and site-to-user options.
FlashFXP can connect to sFTP servers, backup to FTP, edit PHP files and edit HTML documents.
A freeware client with support for FTP, FTPS and SSH.
AnyConnect is software which can connect to sFTP servers.
Bullet Proof FTP is a fully automated FTP client, with many advanced features.
BulletProof FTP Client is software which can connect to sFTP servers.