Hello and Greeting from the SF Bay Area.
Well I don't know how much PSK-31 on VHF you will find in your area BUT if you are looking to get into the Digital Modes the one program that comes to mind is FLdigi at www.w1hkj.com
and download FLdigi. FLmsg and FLwrap. This MultiMode, MultiOS (Windows, Apple Mac OS x and Linux) will do not only PSK-31 but also MT63.
Fldigi is intended for Emcomm usage BUT also does very well for Rag Chewing and soforth. Now onto interfacing.
Well just the CT-44 will not work other than for receiving. You can take the Receive Audio from the 4 pin plug and connect to the Mic Jack on the PC. For Transmitting that is a little bit more involved. If you look at page 11 of the Yaesu User Manual you will see a Capacitor and Resistor network that is required for passing the TX Audio and also for activating the PTT. Also you need some sort of an Interface having a Audio Transformers to Isolate the Radio from the PC. If you are into Home Brewing you might want to checkout the following Website:http://www.qsl.net/wm2u/interface.html
You can also go online and do a search as well. I think one is finding a stand alone 4pin 2.5mm cable will be the challenge other than buying the CT-44 Adapter.
My tired old eyes just read that you are using Ubuntu. Fldigi is just the ticket for you. Also checkout this Yahoo User Group: http://groups.yahoo.com/group/linuxham
You could also just do whats called Acoustical coupling. This is where if you want to receive is put the PC's Mic next to the Radio's Speaker and then for TX the Radio's Mic next to the PC's speakers.
Now in my humble opinion I would work on upgrading my License and get a better Radio.
Drop me a line if you have any other questions.
73 de Steve KB6HOH