I know in Chrome you can clear offline apps by typing this address
chrome://appcache-internals/
Does safari 5.0+ have something similar?
Please note that CTRL+ALT+E will not remove offline web apps from the cache.
On OS X the Safari cache manifest database can be found in
/var/folders/XX/xxxxxx/-Caches-/com.apple.Safari/ApplicationCache.db
where X/x is random characters. (You'll find one set of random characters for each user on your computer; you only need to worry about the path that corresponds to your account.) Delete ApplicationCache.db and restart Safari. (The .db file will regenerate when Safari encounters a site with a cache manifest.)
The easiest way to get at this file is to run the following command in Terminal
defaults write com.apple.Finder AppleShowAllFiles YES
and then force a restart of Finder. When you're done run
defaults write com.apple.Finder AppleShowAllFiles NOand restart Finder again.
I found the seed of this answer here.