When you use RDesktop to remote into another computer, is it traveling over the internet unencrypted? How secure is RDesktop, or should another application be used?
By default all the rdesktop connections are encrypted.
You can use -e, -E option to disable encryption based on your need.
Alternatively you can use
The RDP protocol does encrypt its messages by default as mention in previous answer however latest rdesktop sources does also have support for the RDPv5.2 feature SSL/TLS encryption of the communication which is more commonly used approach of secure transmission.