This is naturally due to the httpModules, httpHandlers and roleManagers set by the Sitecore Web.Config in the root of the website.
The easiest way to get around this (besides installing on another IIS Site, which can be difficult on an XP developer machine) is to put a web.config in the non-Sitecore related web-application that removes all of the modules, managers and handlers set by Sitecore.
For a default installation of the Sitecore 5.3 demo-site, Printers Inc. this would be:
<remove name="SitecoreHttpModule" />
<remove name="SitecoreUploadWatcher" />
<remove name="SitecoreXslWatcher" />
<remove name="SitecoreLayoutWatcher" />
<remove name="SitecoreConfigWatcher" />
<remove name="StatCenterPersonalizer" />
<remove verb="*" path="sitecore_media.ashx"/>
In other installations / versions this might vary a bit, but you can always check the sitecore web.config and see whats added, so you can then remove it.