I am using wss 3.0, is there a way to change default email message content, when new user is added to the sharepoint site.
Yes, there is a way, but it is NOT recommended. You should never edit any of the default files installed by SharePoint. They can be overwritten any time by a service pack or cumulative update.
SharePoint stores most of the text strings it uses in its UI in resx files. These resx files are located in the 12 hive under /Resources. To find out where exactly, search the 12 Hive for the string you want to modify, and you should find the resx file. Often, you'll find at least two files: the base resx file and the resx file associated with a particular language. You should make your change in the language specific version (in this case, core.en-US.resx). One you have made your change, run IISRESET to force SharePoint to re-process the resx file, and you should be in business. The strings will be changed globally.