In Safari version 4.0.4 for the Mac.
Safari menu / Preferences... / Security
Database storage: "None" allowed before asking
Below that you can press the "Show Databases" button.
That lists the databases and includes buttons for "Remove" and "Remove All"
On the iPod Touch go to
Settings / Safari /
Below "Accept Cookies" and above "Clear History" is "Databases >"
Touch that and you are presented with any databases for Safari.
Touch a database and you see "Used" and "Max Size" but, no way to delete the database.
For information on the existence of databases in Safari see
http://www.apple.com/safari/features.html . There are 9 references to "database' the first being in the section titled "HTML5 Offline Support"