You could set up [custom logs][1] in your `httpd-vhosts.conf` depending on the `HTTP_HOST` variable – if your server is an Apache and you use subdomains for each single site.

For sub directories:

    SetEnvIf Request_URI ^sitename1 sitename1
    SetEnvIf Request_URI ^sitename2 sitename2
    CustomLog sitename1.log common env=sitename1
    CustomLog sitename1.log common env=sitename2

_not tested_

  [1]: http://httpd.apache.org/docs/current/mod/mod_log_config.html#customlog