Yes, file encryption can optionally be used to make a backup/upload to S3 more secure. Files can be stored on the Amazon S3 servers encrypted (i.e. at rest).
Server-side encryption is only available starting with s3cmd 1.5.0-beta1.
S3cmd provides two types of file encryption: server-side encryption and client-side encryption.
Server-Side encryption is about data encryption at rest, that is, Amazon S3 encrypts your data as it writes it to disks in its data centers and decrypts it for you when you access it. As long as you authenticate your request and you have access permissions, there is no difference in the way you access encrypted or unencrypted objects. Amazon S3 manages encryption and decryption for you. For example, if you share your objects using a pre-signed URL, the pre-signed URL works the same way for both encrypted and unencrypted objects.
Amazon S3 Server Side Encryption employs strong multi-factor encryption. Amazon S3 encrypts each object with a unique key. As an additional safeguard, it encrypts the key itself with a master key that it regularly rotates. Amazon S3 Server Side Encryption uses one of the strongest block ciphers available, 256-bit Advanced Encryption Standard (AES-256), to encrypt your data.
When you upload one or more objects with S3cmd, you can specify in your request if you want Amazon S3 to save your object data encrypted. To specify that you want Amazon S3 to save your object data encrypted use the flag --server-side-encryption. Server-side encryption is optional. Your bucket might contain both encrypted and unencrypted objects. Encrypted objects are marked automatically with the metadata header x-amz-server-side-encryption set to AES256.
With Client-Side encryption, you add an extra layer of security by encrypting data locally BEFORE uploading the files to Amazon S3. Client-side encryption and server-side encryption can be combined and used together. In S3cmd, client-side encryption is applied by specifying the flag -e or --encrypt.