First,
Unplug yourself from the net, then noone can intrude, and all imminent danger is gone.
Second,
Find out which trojan it is. If you find ziltch on the HDD, take a look at the running proccesses.
Third,
Even a trojan needs a way to start itself. Take a look at http://www.tlsecurity.net/auto.html to find out how. Then delete every option you find beeing used, thus disabling it's capability to run itself.
Fourth,
Get yourself a decent virus-scan and let it run *ALLWAYS*

Fifth,
if you're still nowhere, place your nice install CD in the cr-rom drive and reboot the frigging thing.

Grtz,