We use and recommend WebPosition 4 from Web Trends
WebPosition® 4 offers all of the tools necessary to improve your web site's search engine rankings and increase revenue. WebPosition 4 now includes a summary dashboard, trend graphs, essential off-site metrics (link popularity and search engine saturation reporting) and 200+ new search engines.
WebPosition 4 allows you to:
Report your search engine rankings
Target your keywords
Optimize pages using built-in expertise
Submit URLs to search engines
Analyze conversions using WebTrends