As part of my initial meeting with my prospective clients, I offer a free analysis of their website. Most of the sites that I review have no optimization which is understood, but many sites have issues that hurt the sites chances of getting any rankings. These are top problems that I frequently encounter with websites:
1.        Lack of title tags or duplicate title tags: Search engines still pay attention to title tags and some sites will have no title tag or the company name as the title tag on every page. Not having good descriptive and unique title tags will hamper websites rankings.
2.       Duplicate or missing Meta tag descriptions:   Descriptions don’t help your rankings, but usually show up on the search engine listings.  Duplicate or missing descriptions will cause the search engines to ignore them and to decide on their own what to display on the search listing. In some cases I have seen very unusual or at least very non-compelling listings.
3.       JavaScript menus: The search engines usually find the home page of most websites. If there are no links on the home page body or a site map link, then the search engine would need to follow the menu bar links to find all the other pages, search engines can’t read JavaScript menu’s so in these cases the only page in the search engine index is the home page.
4.       Unreadable Content: Flash, graphics, JavaScript and iframes give search engines a lot of problems. Some sites have very little, if any readable content. Rankings are based on readable content.
5.       Incorrectly set up Robots.txt file:   This file specifically tells what content should NOT be indexed by search engines. Occasionally I see cases where the search engine is instructed to not index the entire site. The webmaster either misunderstood how to use the file, or wanted to temporarily disallow crawling, but forgot to change it.
6.       Dynamically created URLs:   This subject can be pretty complicated, but sometimes I find that search engines do not index certain types of dynamic urls. Here is a source that provides more information Dynamic Solution for Dynamic URLS
If you want to see what pages of your site has been indexed, put “site:www.yourdomain” in the search bar of Google and check what appears. Furthermore, if you click on the “cache” link then click on “text-only version” you will see exactly what the search engine is indexing on your site.