I've run into a problem where I add a web app to my iPad home screen (iOS 5.0.1 iPad 2), and when I open it it appears to be caching something behind the scenes, independent of Safari.
I've cleared out everything from Safari that's available in Settings (Clear History and Clear Cookies & Data), and when I navigate to the web app with Safari I see the app in its current state. However if I open the home screen bookmark I get the app in a pre-changed state.
I've seen a lot of information about using a cache.manifest to cache resources for offline use, but I'm not sure if that's relevant to this since I would like the exact opposite: cache nothing.
I've gone to the level of not even testing external resources; if I change some arbitrary test string in the body element of my index.html, the home screen bookmark does not show the updated text.
Another workaround is to add ?v=1 to your Javascript and CSS links. For example:
<link rel="stylesheet" type="text/css" media="all" href="./css/ipad.css?v=1">
<script src="./js/ipad.js?v=1"></script>
It seems one doesn't have to update the number when your file has changed, as far as I can tell. Apparently, on an iPad 2 with the latest software update installed, it is enough to just hint at something dynamic.