As I said above, removal depends on which flavor of trojan you get infected with. Terminal is the easiest way to deal with this stuff.
Here's what I am suggesting as a rudimentary test for some of the known strains of the flashback trojans. Open a terminal window and copy/paste each of the following lines hitting return after each one and note the results:
defaults read ~/.MacOSX/environment
defaults read /Applications/Safari.app/Contents/Info LSEnvironment
ls -la ~/Library/LaunchAgents
grep "/Users/$USER/\..*" ~/Library/LaunchAgents/*
For the two defaults command if you get anything other than a "does not exist" error message post the results since you are almost certainly infected.
The third command, ls, just lists the contents of your LaunchAgents, if any. That's additional info to be used in conjunction with the last grep command. If the grep shows any results then that too may indicate infection and again post its results.