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Website Analysis Tool

I actually think seositecheckup.com is a great tool for most onsite analysis. It's decent enough to catch what's happening on a broad level of a site/URL.

For checking for bad links I use linkdelete.com but it does block you after a few lookups.

For checking links more in depth I recommend Ahrefs subscription. This will allow you to take a look at all of the websites links.

A free plugin that's pretty good is SEOQuake which will check the PR of all of the SERP results and other metrics which makes it fun to see what's ranking and why from a broad level.
 
You would also like to visit GTmetrix site. Which give you detailed analysis of your website with useful tips for how to fix bad issues of your site.
 
For Web site analysis I prefer gostats because it is fully customized and can gives the statistics information that is most important to web site. Hope this may help you.:)
 
@perrycraft, I'll forgive you for saying google ;) Google has a lot of significant problems that all my affiliate friends are moving away from. (IF you want google to eat your lunch, then please install google on your sites! They will know more about your customer channels than you. Hey maybe when your business gets eaten, google will hire you to mop their floors?)

For alternatives, "go stats" is a good option. I also like to use piwik, but find that managing that software is too costly in house as my sites grow and become more complex.

But aside from everything else, stay away from google. Google is like AIDs for your data... You do not want to get infected and uninstall it as soon as possible and go with something else... anything else!
 
I use Google Analytics for my websites and I'm pretty satisfied...of course, if you want more, you pay more, but it's really worth it.
 
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