Just about everyone has an antivirus (AV) application running on their computers. One job of this software is to detect infected files and deal with them. How the AV software handles a detected infection depends on how the software is configured. It can range from a warning, to putting the file in a "Quarantine" location or deleting the file(s). Every AV package has default rules on how to handle potentially infected files.
One problem that can rise up and bite you is when the AV software thinks a critical file is infected (false positive) and decides to delete it. I've lost count of the number of times that someone reports that a critical database file was deleted after an AV scan.
Another is wasted time scanning files that just are not going to get infected. Even the best AV software will slow down a computer while it is scanning. This applies especially to "Real Time" scanning, where files are scanned before opening them as well as scheduled scans.
While this is usually a server or network concern, it can also affect personal computers, also. For most of us, anything that will speed up our computers is "GOOD".... ;-)
MS has a lot of guidelines for what files & folders to exclude from AV scanning. You can scan their Knowledge Base for them.
This is a pretty comprehensive one that was posted on myITforum. It's a document from MS that gets a bit busy and technical, but is a great resource.
http://myitforum.com/cs2/files/folders/configmgr/entry119487.aspx
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