You need back links and decent ones. Your question is really to broad, as it appears you have specific issues if it is a recurring problem for you.
1. use spiderable navigation
2. if you use flash then use the noscript tag to replicated the flash content (same for video)
3. Make sure your content is unique
4. Use a google sitemap submitted and verified through webmaster tools
5 get some backlinks to the home and inner pages.
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