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NickMorris
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IMO an ‘SEO’ audit should really just deal with issues that will affect organic traffic and if you have expertise in other areas, such as conversion rate optimisation, that should be labeled as such and not lumped in with ‘SEO.’ But I guess that depends on your definitions and processes and those will be different for almost every person.

I’ve separated the SEO audit process into three steps;
1) Website analysis
2) Additional research and analysis
3) Recommendations

I’ve used the word ‘could’ because the more information the better but most businesses, especially small businesses, will be limited by their budgets so an SEO report will likely only focus on a smaller number of aspects.

I’ve also separated ‘onsite’ and ‘offsite’ in a few places.

Website analysis could include;
Onsite
– Keyword targeting
– Technical issues
– Existing Content
– Schema.org markup
– Google Places / Google+ Local
– Existing Data e.g. analytics data
– Services / Scripts / Tools
— Analytics
— Google webmaster tools
— Social sharing buttons
— CMS
— Plugins, themes, extensions

Offsite
– Backlink analysis

Additional research and analysis could include;
– Keyword research and analysis incl. keyword competition
– Competitor website research and analysis
– Market analysis
– How your target market searches (difficult to determine)
– Some of the other purchase process related things that John mentioned in his post

Recommendations could include;
Onsite
– Website changes/redesign/restructure/major update/overhaul incl. change of CMS, themes, plugins etc.
– Changes/additions to services/scripts/tools
– Keyword optimisation
– Additional content
– Ongoing content strategy
– Schema.org markup
– Google Places / Google+ Local optimisation

Offsite
– Link building strategy
– Social sharing strategy

As John mentioned, the word ‘keyword’ can be confusing. I use it to refer any one or string of individual words that could be searched for.

Its worth pointing out that different aspects will have different effects on different websites.
– Large websites including e-commerce sites can suffer significantly from technical issues
– E-commerce sites in particular often suffer from lack of original content
– Small websites can suffer from lack of content and poor keyword optimisation
– In competitive industries the quality and number of backlinks will play a more important role

I think this ‘technical site audit checklist’ is a good resource: http://www.seomoz.org/blog/how-to-do-a-site-audit