Are there any hooks that get called before modules are loaded? There are a few user tracking checks I would like to perform before the site main page gets loaded. I don't really want to have to wait for drupal to load all the modules and start running the theme code before I do this.

Are there any hooks that can be overwritten to perform my checks?
I don't recommend using hook_init() as it doesn't run on cached pages. Try using hook_boot(). As per the documentation it runs at the beginning of the page request when Drupal is still in the bootstrap. Hope this helps!