i\'m trying to track a NullReferenceException that shows up on sitecore 6.5 at loading any webpage:
[NullReferenceException: Object reference not set to an i
Looks like an "include" config file is missing from your setup. Decompile Sitecore.Resources.Media.UploadWatcher.InitializeIgnoreList to try to work out which one (sorry haven't got a decompiler handy). Reflector comes with a 30-day trial or Telerik Just Decompile is free.
EDIT I use a product called SlowCheetah which does XML transformations based on build configuration for any XML file, not just web.config like VS does. You can NuGet it. Highly Recommended.