Copyscape is the leading online duplicate detection solution, it allows you to check the content of your site for duplication, and now, with the addition of private index functionality, you can also scan for canonical content within your own domain.
Plagium is another good duplicate content detection tool, but as opposed to copyscape which checks Google's index primarily, and Yahoo's index when the batch search function is used, Plagium only checks Yahoo. Therefore if you have duplicate content problems I would recommend using copyscape primarily. This tool was included as unlike copyscape it is 100% free and without limitation.
A great little tool for finding out what type of server your site is hosted on, ideally for SEO, this should return Linux/Apache, if your site is hosted on any type of windows server I would recommned you stringly consider moving to Apache/Linux hosting! Windows servers do not support case sensitive urls which can lead to canonicalisation problems.
Another useful SEO tool, the check server headers tool allows you to make sure that your pages are returning the correct HTTP status code, great for checking problematic "not found" pages.
A great firefox addon which allows you to see your website exactly as googlebot. Essential for carrying out audits and particularly useful for revealing cloaked text. Compare what you see with the plugin activated and set to googlebot against what is displayed by your browsers default user agent.