One of the great things going for VOIP is the freely available Asterisk PBX. Using Asterisk, you can turn your Desktop, Laptop... or PDA... into a featured telephone system with support for voice menus, voicemail, faxing, and many more interesting things.
Asterisk recently released an update to the 1.6 line, which already includes support for encrypted SIP and TCP connections. However, one third-party module that provides fax detection over SIP and IAX (basically, Voice Over IP/VOIP traffic), no longer works smoothly with the most recent versions.
At work we help our clients to do a lot of creative things using Asterisk and other systems we custom design. One slowdown to adopting the new versions of Asterisk, is that Newman Telecom's NVFaxDetect hasn't yet been ported for use with new versions of Asterisk. If a port has been created, it isn't easily found through public channels at present.
We're now porting our own open-source faxing implementation based on the app_rxfax and app_txfax libraries with spandsp. Here's hoping this development will be preempted by a digium or other community release!