I always advocate in-house maintenance of search engine optimisation (unless you have plenty of money to outsource it properly), so any analysis tools to highlight problems are always helpful. One really worth looking at is SEO Analyzer, which will spend three minutes getting data from your website and presenting you with an action plan.
The best way to see what SEO Analyzer does is to use it, but you get scores for your on-page SEO, traffic, keywords and backlinks, and a ‘health check’ from a crawl of 100 pages. If you don’t find anything useful in there, I’d be very surprised.