The 'Top Sites' database is located in user profile directory, the default one is ' ~/.config/chromium/Default/Top Sites' (for chrome: ~/.config/google-chrome/default, in windows C:\Documents and Settings\%USERNAME%\Local Settings\Application Data\Google\Chrome\User Data\Default). 'Most Visited' section on new tab in Chrome/Chromium can be edited by hand, by directly changing 'Top Sites' sqlite3 database inside Chrome/Chromium with sqlite3 and SQL (or by any other sqlite3 db editor, like sqlitebrowser).
