First, trojans and viruses are two entirely different things. May as well toss worms in there two. That, and the fact that all three are bad, is about all you need to know about them.
Except that the only absolutely sure way to be sure you're rid of a trojan is to format. Otherwise, you never know if it left some other little present on your system in some place that virus scanners can't search (like the system restore area), or maybe it altered your virus scanner to hide itself from detection. You can never know for sure until you format. This applies to whatever system you're dealing with as well... Windows, Mac, Unix workstation/server... There's never a way to be absolutely sure something's gone without formatting.