removing is one thing, but detection is another thing. It also really depends on which trojan and which OS. There is a trojan for unix/linux which is very hard to detect. As far as i'm aware, theres only one tool to find that specific trojan. Its a very rare trojan, actually its a lot more than a simple trojan. It does not sit and listen on a port like other trojans, it does not show up on any process listing, it only shows up with its antidode. This trojan is called KIS (kernel intrusion system) made by 0ptyx. Its by far the most advanced trojan tool i have ever seen. It acutally sits inside the kernel itself. Even IDS cannot pick up the setup of this trojan. On the other hand, normal users have nothing to fear, since the trojan KIS is used very rarely and its target is mainly very high security boxes. I have never heard of this trojan infecting a home user, or even a small private company.
For the normal common trojans on windows systems, there are some excellent tools to remove them. I always recomend a look at aswell as getting adaware. Netstat is also helpful, since it shows which ports are in st On the other hand, on windows it normally takes user error to get infected by a trojan, as in lack of antivirus, lack of knowledge, by just clickin on files where you have no idea what they are etc.....