It's always bothered me that Google Analytics (and similar embedded web traffic monitoring services) can only see a reflection of the traffic going to my server and can only see page visits. If I want to track real downloads of a software package, there's no way Google Analytics can possibly tell me that because its javascript can't be attached to a ZIP file. Is there a way I can upload my log files to Google so that the pointy-haired boss can see downloads of our ZIP/PDF/BIN files and not just visits to the download page?
No, but there is an entire segment of analytics tools that can do whats called 'log analysis'. Take a look at tools like Splunk (really pretty pointy hair reports available here) or Graylog2.