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Thanks Alan, you are right this site has quite a long way to go. The first crawl was just finished and I notice that the most errors were due to dupe content so I decided I would try and tackle that first. Thank you for all the pointers, I will be taking a look at all those as soon as I can.
When the crawl diagnostics came back for my site its showing around 3,000 pages of duplicate content. Almost all of them are of the catalog search results page. I also did a site search on Google and they have most of the results pages in their index too. I think I should just disallow the bots in the /catalogsearch/ sub folder, but I'm not sure if this will have any negative effect?
I would at least nofollow all the links, 100 external links is getting up there. In the crawl diagnostics on SEOmoz if a page has over 100 links it gets a warning letting you know that there are too many links on the page.
7/28/2011 When SEOmoz launched the Keyword Difficulty Tool I think we were all impressed with the reports that it was able to spit out. For me having all the data in one place was very useful except for when I tried to share it. At the moment the only way to share it is by exporting it as a .csv and then it just becomes a block of data.