There are many potential issues involving your content so you should check them thoroughly. For example, if your content can't be found or understood by the search engine-- it will definitely work against you.
Some examples are:
- Orphaned content that can't be found by the search engine
- Content that is only available by doing a site search
- Any element that uses Flash or Java
- Audio files
- Video files
- The usage of frames or content embedded from another site
- Content that split into subdomains instead of sub-folders
Search engines care if your content is easily discoverable, understandable and fits in the overall structure of your website. Just make sure that everything makes sense and that your website is organised and you should be fine.