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Basics of Trojan/Virus
There's a lot of different aspects to virus removal and I'm not going to cover them all here. If you're looking for a good guide to antivirus software, we've got one. I have another article on the usefulness of AVG antivirus software. Here, I'll discuss if it's better to quarantine or delete a Trojan virus.
Just as a quite note, Trojans and viruses are basically the same thing for our purposes. A Trojan acts like its namesake, the Trojan horse, to allow another person to sneak into your system. A virus is a much more versatile term, but it's basically just a piece of destructive software that can either steal information or change your computer or browser to act in a way that the hostile programmer wants.
Now on to the basic and the difference between quarantining a virus and deleting a virus.
Just to start off from the very beginning, let's take a look at the usual virus removal process. You will probably get these options through the alert system in your antivirus software. Either through the real time shield or an active scan, if it spots what looks like an infected file, it will bring up an interface. It should give a list of options ranging from ignore to a complete deletion. The better software will make this a simple click to either ignore, quarantine or delete the virus. Some will offer instant access to an online database while others will require you to copy it down.
The only real question is what you want to do with the file once you've received the alert.
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Why You Should Quarantine a Virus/Trojan
Quarantine does what it says. It will wall off the infected program and make sure that it can't affect the rest of your system. Most antivirus software will do this through a special virus chest that you can access through the program.
You're basically safe once the virus or Trojan has been quarantined. If your program is any good, then that infected file is as good as if it had been deleted. It is still on the system though and you will probably want to wipe it out at some point in the future.
Why should you quarantine a virus/Trojan? Well, there are some benefits to a temporary quarantine. The big benefit is that you still have a copy to play around with, but it's in a safe format. You can check the name and analyze it a little more.
Once a Trojan or virus is quarantined, you should do some quick Googling for the name. There are a few good databases of viruses out there. What you really want to get is confirmation that it's infected. A lot of antivirus programs will have occasional false positives. I had one a few months ago, where the DRM on a steam copy of X-COM was enough to trigger an alert. Until you can confirm that the file is really infected, you should just quarantine it. If it's a false alarm, then you can restore it to it's rightful place.
Of course, there isn't much of a reason to just leave a virus in the virus chest either. Once it's confirmed as infected, you should really delete it.
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Why You Should Delete a Virus/Trojan
As I just covered, all infected files should be deleted eventually. Viruses, Trojans, and malware can often only be handled by deleting the infection. You can't just press a little button to "scrub" the system. Occasionally viruses will contaminate normal programs and you will be able to just clean away the infection, but this is getting to be the exception. Trojans and viruses are often just poison for the system. They can only be cleared away. Any damaged software will have to be downloaded again.
That's actually all there is to deletion. A good antivirus program should properly shred them so that they're gone for good. You should probably check to make sure that it isn't hanging around in the system waiting to reinstall itself, but that's an entirely different subject. You should know all the reasons to either delete or quarantine a Trojan virus.
For more information, read How Do I Get Rid of a Trojan Horse Virus, by Lee Clemmer.