OSX 10.5.7 Safari 4.0.2
$HOME/Library/Caches/com.apple.PubSubAgent
$HOME/Library/Caches/com.apple.Safari
$HOME/Library/Caches/Metadata/Safari
$HOME/Library/Cookies/Cookies.plist ###
$HOME/Library/Preferences/com.apple.Safari.plist ###
$HOME/Library/Preferences/com.apple.Safari.RSS.plist
$HOME/Library/PubSub
$HOME/Library/Safari/Bookmarks.plist ###
$HOME/Library/Safari/Downloads.plist
$HOME/Library/Safari/History.plist
$HOME/Library/Safari/HistoryIndex.sk
$HOME/Library/Safari/Form\ Values
$HOME/Library/Safari/LastSession.plist
$HOME/Library/Safari/LocalStorage
$HOME/Library/Safari/TopSites.plist
$HOME/Library/Safari/WebpageIcons.db ###
###をDesktopに出して、他は消去してからSafariを試して下さい。
4つのFileを1つずつ入れて確認して問題があるFileを作り直して下さい。
なお、一番大事なのはBookmarks.plistです。