All user's can be traced, your concern would be encryption and never passing keys over the public medium. If you are using vpn software to connect to private addresses, etc....then you are using a tunneling.
There is no more Microsoft Internet Directory, it's be superceded in technology by Microsoft Messenger, etc...
if you are just connecting to another IP address, directly, and you aren't using tunneling or encryption methods, then are about as secure as your internet connection, but the traffic can still be decoded by a third party and read.
You really want security over Direct connections, you should look into VPN and encryption methods.
The application can have holes in it, if the original packet is encapsulated with something that is secure.
Through a direct connection, you aren't using an Internet Server as a relay point for traffic, Netmeeting allows a user to connect directly to your desktop.....