Take a look at "IBP" the software covers what you want to do and more. visit the site and if you like but cannot afford the fancy price tag just google the following "ibp blackhatworld.com" they have free copies available Good Luck
There are so many different areas you might want to look at: 1) On page factors 2) Inbound link counts (and ideally quality) 3) Current rankings for keywords in main search engines 4) Traffic from natural search by keyword 5) Conversion from natural search by keyword There are tools available for all of these different areas - depending on how deep you need to go. The last two can be covered off by analytics usually (although note they'll be slightly lower than reality because of referrer problems). Rankings can be done by any number of free tools. Inbound link counts can be done by Yahoo SiteExplorer, or something like Majestic SEO or SEOMoz LinkScape (expensive). I run a company that does free on-page SEO scans (see the footer) but there are more out there too depending on your needs - WebCEO for example.
In onpage optimizations you might want to look at bellow factors. 1. Domain Check 2. Server info 4. Website Status in Search Engine 5. Image Optimizations 6. HTML validations and corrections 7. HTML validations and corrections 8. In bound links 9. out bound links 10. keyword analysis 11. Meta tags Writting reports
You need to check keyword position and visitor's overview. I suggest you to use google analytics, its the best tool for seo report.